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Sample records for pts system-an nmr

  1. Mechanism of phosphoryl transfer and protein-protein interaction in the PTS system-an NMR study

    SciTech Connect

    Rajagopal, P.; Klevit, R.E.

    1994-12-01

    HPr and Enzyme IIA{sup Glc} are two of the components of the bacterial PTS (phosphoenolpyruvate: sugar phosphotranferase system) and are involved in the phosphorylation and concomitant translocation of sugars across the membrane. These PTS protein complexes also regulate sugar transport. HPr, phosphorylated at a histidine N1 site by Enzyme I and phosphoenol pyruvate, transfers the phosphoryl group to a histidine N3 position in Enzyme IIA{sup Glc}. HPrs from Gram-positive bacteria undergo regulatory phosphorylation at Ser{sup 46}, whereby phosphorylation of the histidine residue is inhibited. Conversely, histidine phosphorylation inhibits phosphorylation at Ser{sup 46}. HPrs from Gram-negative bacteria possess a serine residue at position 46, but do not undergo regulatory phosphorylation. HPr forms an open-faced sandwich structure with a four-strand S-sheet and 2 to 3 helices lying on top of the sheet. The active-site histidine and Ser{sup 46} occur in conformationally flexible regions. P-His-HPr from the Gram-positive bacterium Bacillus subtilus has been investigated by both homonuclear and heteronuclear two-dimensional and three-dimensional NMR experiments using an in-situ enzymatic regeneration system to maintain a constant level of P-His-HPr. The results show that localized conformational changes occur in the vicinity of the active-site histidine and also near Ser{sup 46}. HPr-Enzyme IIA{sup Glc} complexes from both Bacillus subtilis and Gram-negative Escherichia coli were also studied by a variety of {sup 15}N-edited two-dimensional NMR experiments, which were performed on uniformly {sup 15}N-labeled HPr complexed to unlabeled Enzyme IIA{sup Glc}. The complex is in fast exchange with a molecular weight of about 27 kDa. The focus of our work is to assess the changes undergone by HPr (the smaller of the two components), and so all the experiments were performed with excess Enzyme IIA present in the system.

  2. Endosafe(R)-Portable Test System (PTS)

    NASA Technical Reports Server (NTRS)

    Maule, Jake; Wainwright, Norm; Burbank, Dan

    2005-01-01

    The Portable Test System (PTS) is a hand-held device for monitoring the presence of potentially hazardous bacteria in the environment. It uses an immunological method derived from the horseshoe crab (Limulus polyphemus) to detect bacterial cell membranes and other molecular components of a cell. Further modifications of the PTS will allow detection of individual hazardous species of bacteria. This study was a follow-up of previous PTS and other immunological tests performed on the KC-135 during 2002-2003 (Maule et al., 2003, J. Gravit. Physiol.) and in the underwater habitat Aquarius during NEEMO 5 (Maule et al., 2005, Appl. Environ. Microbiol in prep.). The experiments described here were part of a final testing phase prior to use of the PTS on the International Space Station (ISS), scheduled for launch on 12A.1 on February 9th 2006. The specific aspects of PTS operation studied were those involving a fluid component: pumping, mixing, incubations and pipetting into the instrument. The PTS uses a stepper motor to move fluid along small channels, which may be affected by reduced gravity.

  3. Mechanistic Insights into PTS2-mediated Peroxisomal Protein Import

    PubMed Central

    Kunze, Markus; Malkani, Naila; Maurer-Stroh, Sebastian; Wiesinger, Christoph; Schmid, Johannes A.; Berger, Johannes

    2015-01-01

    The destination of peroxisomal matrix proteins is encoded by short peptide sequences, which have been characterized as peroxisomal targeting signals (PTS) residing either at the C terminus (PTS1) or close to the N terminus (PTS2). PTS2-carrying proteins interact with their cognate receptor protein PEX7 that mediates their transport to peroxisomes by a concerted action with a co-receptor protein, which in mammals is the PTS1 receptor PEX5L. Using a modified version of the mammalian two-hybrid assay, we demonstrate that the interaction strength between cargo and PEX7 is drastically increased in the presence of the co-receptor PEX5L. In addition, cargo binding is a prerequisite for the interaction between PEX7 and PEX5L and ectopic overexpression of PTS2-carrying cargo protein drastically increases the formation of PEX7-PEX5L complexes in this assay. Consistently, we find that the peroxisomal transfer of PEX7 depends on cargo binding and that ectopic overexpression of cargo protein stimulates this process. Thus, the sequential formation of a highly stable trimeric complex involving cargo protein, PEX7 and PEX5L stabilizes cargo binding and is a prerequisite for PTS2-mediated peroxisomal import. PMID:25538232

  4. Cerebral blood flow in patients (PTS) exposed to neurotoxic chemicals

    SciTech Connect

    Heuser, G.; Mena, I.; Thomas, C.

    1994-05-01

    Exposure to neurotoxic chemicals as pesticides, glues, solvents, etc. are known to induce neurologic and psychiatric symptomatology. We report on 72 pts, 33 young pts, 8 males, and 26 females, age 55 (7) yrs, 15 of them exposed to pesticides, and 37 to solvents. They were studied with quantitative and qualitative analysis of rCBF performed with 30 mCi of Xe-133 (Xe) by inhalation followed by 30 mCi of Tc-HMPAO given IV. Imaging was performed with a brain dedicated system, and distribution of rCBF was assessed with automatic ROI definition, and HMPAO normalized to maximal pixel activity in the brain. Results of Xe rCBF are expressed as mean and (S.D.) in ml/min/100g, and HMPAO as mean and (S.D.) uptake per ROI and compared with age-matched controls, 10 young and 20 elderly individuals, and also to a group of 36 elderly chronic fatigue pts (CFS), and 26 depression pts. CBF was diminished in young and elderly, 45 (7) and 40 (7) ml/min 100g, p<0.02 for both groups. Thus we conclude that pts exposed to chemicals present with diminished CBF, worse in elderly in the right dorsal frontal and parietal lobes, and in young, in left dorsal frontal and temporal lobes. These findings are significantly different from observations in pts and chronic fatigue and depression.

  5. Current pulse shaping of the load current on PTS

    NASA Astrophysics Data System (ADS)

    Xia, Minghe; Li, Fengping; Ji, Ce; Wei, Bing; Feng, Shuping; Wang, Meng; Xie, Weiping

    2016-02-01

    The typical rise time of PTS machine is ˜110 ns with about 10 MA peak current under short pulse mode when all 24 modules discharge simultaneously. By distributing the trigger times of 12 laser beams logically and adjusting the statues of the pulse output switches, longer rise-time pulse can be obtained on the PTS facility. Based on the required pulse shape, whole circuit simulations will be used to calculate the trigger times of each laser triggering gas switch and the status of the pulse output switches. The rise time of the current is determined by the time difference between the first and last trigged laser triggering gas switches. In order to trigger the laser triggering gas switch, sufficient laser power is needed to be sent into the gap of the gas switches. The gas pressure and voltage difference on the two electrodes of the gas switches also affect the triggering of the gas switches, and the voltage added on the gas switch is determined by its transition time. Traditionally the trigger time difference should be less than the transition time of the two neighboring modules. A new simulation model of PTS shows one can break this transition time limits. Series of current pulse shaping experiments have been investigated on the PTS (Primary Test Stand). As results, more than 5 MA peak current were successfully achieved on the load with a rise time of 600 ns. This study and experiments of the pulse shaping on PTS demonstrate the adaptable ability of the PTS for offering different waveform of mega ampere current pulse for different research purpose.

  6. Diagnostics for Z-pinch implosion experiments on PTS

    SciTech Connect

    Ren, X. D. Huang, X. B. Zhou, S. T. Zhang, S. Q. Dan, J. K. Li, J. Cai, H. C. Wang, K. L. Ouyang, K. Xu, Q. Duan, S. C. Chen, G. H. Wang, M. Feng, S. P. Yang, L. B. Xie, W. P. Deng, J. J.

    2014-12-15

    The preliminary experiments of wire array implosion were performed on PTS, a 10 MA z-pinch driver with a 70 ns rise time. A set of diagnostics have been developed and fielded on PTS to study pinch physics and implosion dynamics of wire array. Radiated power measurement for soft x-rays was performed by multichannel filtered x-ray diode array, and flat spectral responses x-ray diode detector. Total x-ray yield was measured by a calibrated, unfiltered nickel bolometer which was also used to obtain pinch power. Multiple time-gated pinhole cameras were used to produce spatial-resolved images of x-ray self-emission from plasmas. Two time-integrated pinhole cameras were used respectively with 20-μm Be filter and with multilayer mirrors to record images produced by >1-keV and 277±5 eV self-emission. An optical streak camera was used to produce radial implosion trajectories, and an x-ray streak camera paired with a horizontal slit was used to record a continuous time-history of emission with one-dimensional spatial resolution. A frequency-doubled Nd:YAG laser (532 nm) was used to produce four frame laser shadowgraph images with 6 ns time interval. We will briefly describe each of these diagnostics and present some typical results from them.

  7. The unique degradation pathway of the PTS2 receptor, Pex7, is dependent on the PTS receptor/coreceptor, Pex5 and Pex20

    PubMed Central

    Hagstrom, Danielle; Ma, Changle; Guha-Polley, Soumi; Subramani, Suresh

    2014-01-01

    Peroxisomal matrix protein import uses two peroxisomal targeting signals (PTSs). Most matrix proteins use the PTS1 pathway and its cargo receptor, Pex5. The PTS2 pathway is dependent on another receptor, Pex7, and its coreceptor, Pex20. We found that during the matrix protein import cycle, the stability and dynamics of Pex7 differ from those of Pex5 and Pex20. In Pichia pastoris, unlike Pex5 and Pex20, Pex7 is constitutively degraded in wild-type cells but is stabilized in pex mutants affecting matrix protein import. Degradation of Pex7 is more prevalent in cells grown in methanol, in which the PTS2 pathway is nonessential, in comparison with oleate, suggesting regulation of Pex7 turnover. Pex7 must shuttle into and out of peroxisomes before it is polyubiquitinated and degraded by the proteasome. The shuttling of Pex7, and consequently its degradation, is dependent on the receptor recycling pathways of Pex5 and Pex20 and relies on an interaction between Pex7 and Pex20. We also found that blocking the export of Pex20 from peroxisomes inhibits PTS1-mediated import, suggesting sharing of limited components in the export of PTS receptors/coreceptors. The shuttling and stability of Pex7 are divergent from those of Pex5 and Pex20, exemplifying a novel interdependence of the PTS1 and PTS2 pathways. PMID:25009284

  8. A probabilistic approach to the evaluation of the PTS issue

    SciTech Connect

    Cheverton, R.D.; Selby, D.L.

    1991-01-01

    An integrated probabilistic approach for the evaluation of the pressurized-thermal-shock (PTS) issue was developed at the Oak Ridge National Laboratory (ORNL) at the request of the Nuclear Regulatory Commission (NRC). The purpose was to provide a method for identifying dominant plant design and operating features, evaluating possible remedial measures and the validity of the NRC PTS screening criteria, and to provide an additional tool for estimating vessel life expectancy. The approach was to be integrated in the sense that it would include the postulation of transients; estimates of their frequencies of occurrence; systems analyses to obtain the corresponding primary-system pressure, down-comer coolant temperature, and fluid-film heat-transfer coefficient adjacent to the vessel wall; and a probabilistic fracture-mechanics analysis, using the latter data as input. A summation of the products of frequency of transient and conditional probability of failure for all postulated transients provides an estimate of frequency of vessel failure. In the process of developing the integrated pressurized-thermal-shock (IPTS) methodology, three specific plant analyses were conducted. The results indicate that the NRC screening criteria may not be appropriate for all US pressurized water reactor (PWR) plants; that is, for some PWRs, the calculated mean frequency of vessel failure corresponding to the screening criteria may be greater than the maximum permissible value in Regulatory Guide 1.154. A recent view of the ORNL IPTS study, which was completed in 1985, indicates that there are a number of areas in which the methodology can and should be updated, but it is not clear whether the update will increase or decrease the calculated probabilities. 31 refs., 2 tabs.

  9. Application of probabilistic fracture mechanics to the PTS issue

    SciTech Connect

    Cheverton, R.D.; Ball, D.G.

    1985-01-01

    As a part of the NRC effort to obtain a resolution to the PWR PTS issue, a probabilistic approach has been applied that includes a probabilistic fracture-mechanics (PFM) analysis. The PFM analysis is performed with OCA-P, a computer code that performs thermal, stress and fracture-mechanics analyses and estimates the conditional probability of vessel failure, P(F/E), using Monte Carlo techniques. The stress intensity factor (K/sub I/) is calculated for two- and three-dimensional surface flaws using superposition techniques and influence coefficients. Importance-sampling techniques are used, as necessary, to limit to a reasonable value the number of vessels actually calculated. Analyses of three PWR plants indicate that (1) the critical initial flaw depth is very small (5 to 15 mm), (2) the benefit of warm prestressing and the role of crack arrest are transient dependent, (3) crack arrest does not occur for the dominant transients, and (4) the single largest uncertainty in the overall probabilistic analysis is the number of surface flaws per vessel. 30 refs., 6 figs., 4 tabs.

  10. PredPlantPTS1: A Web Server for the Prediction of Plant Peroxisomal Proteins

    PubMed Central

    Reumann, Sigrun; Buchwald, Daniela; Lingner, Thomas

    2012-01-01

    Prediction of subcellular protein localization is essential to correctly assign unknown proteins to cell organelle-specific protein networks and to ultimately determine protein function. For metazoa, several computational approaches have been developed in the past decade to predict peroxisomal proteins carrying the peroxisome targeting signal type 1 (PTS1). However, plant-specific PTS1 protein prediction methods have been lacking up to now, and pre-existing methods generally were incapable of correctly predicting low-abundance plant proteins possessing non-canonical PTS1 patterns. Recently, we presented a machine learning approach that is able to predict PTS1 proteins for higher plants (spermatophytes) with high accuracy and which can correctly identify unknown targeting patterns, i.e., novel PTS1 tripeptides and tripeptide residues. Here we describe the first plant-specific web server PredPlantPTS1 for the prediction of plant PTS1 proteins using the above-mentioned underlying models. The server allows the submission of protein sequences from diverse spermatophytes and also performs well for mosses and algae. The easy-to-use web interface provides detailed output in terms of (i) the peroxisomal targeting probability of the given sequence, (ii) information whether a particular non-canonical PTS1 tripeptide has already been experimentally verified, and (iii) the prediction scores for the single C-terminal 14 amino acid residues. The latter allows identification of predicted residues that inhibit peroxisome targeting and which can be optimized using site-directed mutagenesis to raise the peroxisome targeting efficiency. The prediction server will be instrumental in identifying low-abundance and stress-inducible peroxisomal proteins and defining the entire peroxisomal proteome of Arabidopsis and agronomically important crop plants. PredPlantPTS1 is freely accessible at ppp.gobics.de. PMID:22969783

  11. Moving NMR

    NASA Astrophysics Data System (ADS)

    Blümich, Bernhard; Casanova, Federico; Danieli, Ernesto; Gong, Qingxia; Greferath, Marcus; Haber, Agnes; Kolz, Jürgen; Perlo, Juan

    2008-12-01

    Initiated by the use of NMR for well logging, portable NMR instruments are being developed for a variety of novel applications in materials testing and process analysis and control. Open sensors enable non-destructive testing of large objects, and small, cup-size magnets become available for high throughput analysis by NMR relaxation and spectroscopy. Some recent developments of mobile NMR are reviewed which delineate the direction into which portable NMR is moving.

  12. PTS phosphorylation of Mga modulates regulon expression and virulence in the group A streptococcus.

    PubMed

    Hondorp, Elise R; Hou, Sherry C; Hause, Lara L; Gera, Kanika; Lee, Ching-En; McIver, Kevin S

    2013-06-01

    The ability of a bacterial pathogen to monitor available carbon sources in host tissues provides a clear fitness advantage. In the group A streptococcus (GAS), the virulence regulator Mga contains homology to phosphotransferase system (PTS) regulatory domains (PRDs) found in sugar operon regulators. Here we show that Mga was phosphorylated in vitro by the PTS components EI/HPr at conserved PRD histidines. A ΔptsI (EI-deficient) GAS mutant exhibited decreased Mga activity. However, PTS-mediated phosphorylation inhibited Mga-dependent transcription of emm in vitro. Using alanine (unphosphorylated) and aspartate (phosphomimetic) mutations of PRD histidines, we establish that a doubly phosphorylated PRD1 phosphomimetic (D/DMga4) is completely inactive in vivo, shutting down expression of the Mga regulon. Although D/DMga4 is still able to bind DNA in vitro, homo-multimerization of Mga is disrupted and the protein is unable to activate transcription. PTS-mediated regulation of Mga activity appears to be important for pathogenesis, as bacteria expressing either non-phosphorylated (A/A) or phosphomimetic (D/D) PRD1 Mga mutants were attenuated in a model of GAS invasive skin disease. Thus, PTS-mediated phosphorylation of Mga may allow the bacteria to modulate virulence gene expression in response to carbohydrate status. Furthermore, PRD-containing virulence regulators (PCVRs) appear to be widespread in Gram-positive pathogens. PMID:23651410

  13. Chromatographic NMR in NMR solvents

    NASA Astrophysics Data System (ADS)

    Carrara, Caroline; Viel, Stéphane; Delaurent, Corinne; Ziarelli, Fabio; Excoffier, Grégory; Caldarelli, Stefano

    2008-10-01

    Recently, it was demonstrated that pseudo-chromatographic NMR experiments could be performed using typical chromatographic solids and solvents. This first setup yielded improved separation of the spectral components of the NMR spectra of mixtures using PFG self-diffusion measurements. The method (dubbed Chromatographic NMR) was successively shown to possess, in favorable cases, superior resolving power on non-functionalized silica, compared to its LC counterpart. To further investigate the applicability of the method, we studied here the feasibility of Chromatographic NMR in common deuterated solvents. Two examples are provided, using deuterated chloroform and water, for homologous compounds soluble in these solvents, namely aromatic molecules and alcohols, respectively.

  14. The peroxisomal receptor Pex19p forms a helical mPTS recognition domain

    PubMed Central

    Schueller, Nicole; Holton, Simon J; Fodor, Krisztian; Milewski, Morlin; Konarev, Petr; Stanley, Will A; Wolf, Janina; Erdmann, Ralf; Schliebs, Wolfgang; Song, Young-Hwa; Wilmanns, Matthias

    2010-01-01

    The protein Pex19p functions as a receptor and chaperone of peroxisomal membrane proteins (PMPs). The crystal structure of the folded C-terminal part of the receptor reveals a globular domain that displays a bundle of three long helices in an antiparallel arrangement. Complementary functional experiments, using a range of truncated Pex19p constructs, show that the structured α-helical domain binds PMP-targeting signal (mPTS) sequences with about 10 μM affinity. Removal of a conserved N-terminal helical segment from the mPTS recognition domain impairs the ability for mPTS binding, indicating that it forms part of the mPTS-binding site. Pex19p variants with mutations in the same sequence segment abolish correct cargo import. Our data indicate a divided N-terminal and C-terminal structural arrangement in Pex19p, which is reminiscent of a similar division in the Pex5p receptor, to allow separation of cargo-targeting signal recognition and additional functions. PMID:20531392

  15. Characterization, prediction and evolution of plant peroxisomal targeting signals type 1 (PTS1s).

    PubMed

    Reumann, S; Chowdhary, G; Lingner, T

    2016-05-01

    Our knowledge of the proteome of plant peroxisomes and their functional plasticity is far from being complete, primarily due to major technical challenges in experimental proteome research of the fragile cell organelle. Several unexpected novel plant peroxisome functions, for instance in biotin and phylloquinone biosynthesis, have been uncovered recently. Nevertheless, very few regulatory and membrane proteins of plant peroxisomes have been identified and functionally described up to now. To define the matrix proteome of plant peroxisomes, computational methods have emerged as important powerful tools. Novel prediction approaches of high sensitivity and specificity have been developed for peroxisome targeting signals type 1 (PTS1) and have been validated by in vivo subcellular targeting analyses and thermodynamic binding studies with the cytosolic receptor, PEX5. Accordingly, the algorithms allow the correct prediction of many novel peroxisome-targeted proteins from plant genome sequences and the discovery of additional organelle functions. In this review, we provide an overview of methodologies, capabilities and accuracies of available prediction algorithms for PTS1 carrying proteins. We also summarize and discuss recent quantitative, structural and mechanistic information of the interaction of PEX5 with PTS1 carrying proteins in relation to in vivo import efficiency. With this knowledge, we develop a model of how proteins likely evolved peroxisomal targeting signals in the past and still nowadays, in which order the two import pathways might have evolved in the ancient eukaryotic cell, and how the secondary loss of the PTS2 pathway probably happened in specific organismal groups. PMID:26772785

  16. A Novel PTS of Streptococcus mutans is Responsible for Transport of Carbohydrates with α-1,3 linkage

    PubMed Central

    Ajdic, Dragana; Chen, Zhiyun

    2012-01-01

    SUMMARY The most common type of carbohydrate-transport system in Streptococcus mutans is the phosphoenolpyruvate (PEP)-sugar phosphotransferase system (PTS). We previously showed that fourteen PTSs exist in S. mutans UA159 (Ajdic et al., 2002). Several studies have shown that microorganisms growing in biofilms express different genes as compared to their planktonic counterparts. In this study, we showed that one PTS of S. mutans was expressed in sucrose-grown biofilms. Furthermore, the same PTS was also responsible for the transport and metabolism of disaccharide nigerose (3-O-α-D-glucopyranosyl-D-glucose). Additionally, the results indicate that the studied PTS might be involved in the transport and metabolism of carbohydrates synthesized by glucosyltransferase B (GtfB) and glucosyltransferase C (GtfC) of S. mutans. To our knowledge, this is the first report that shows PTS transport of a disaccharide (and possibly extracellular oligosaccharides) with α-1,3 linkage. PMID:23193985

  17. Synthesis and Physicochemical Characterization of D-Tagatose-1-phosphate: The Substrate of the Tagatose-1-Phosphate Kinase TagK in the PTS-mediated D-Tagatose Catabolic Pathway of Bacillus licheniformis

    PubMed Central

    Van der Heiden, Edwige; Delmarcelle, Michaël; Simon, Patricia; Counson, Melody; Galleni, Moreno; Freedberg, Darón I.; Thompson, John; Joris, Bernard; Battistel, Marcos D.

    2015-01-01

    We report the first enzymatic synthesis of D-tagatose-1-phosphate (Tag-1P) by the multi-component PEP-dependent:tag-PTS present in tagatose-grown cells of Klebsiella pneumoniae. Physicochemical characterization by 31P and 1H NMR spectroscopy reveals that, in solution, this derivative is primarily in the pyranose form. Tag-1P was used to characterize the putative tagatose-1-phosphate kinase (TagK) of the Bacillus licheniformis PTS-mediated D-Tagatose catabolic Pathway (Bli-TagP). For this purpose, a soluble protein fusion was obtained with the 6 His-tagged trigger factor (TFHis6) of Escherichia coli. The active fusion enzyme was named TagK-TFHis6. Tag-1P and D-fructose-1-phosphate (Fru-1P) are substrates for the TagK-TFHis6 enzyme, whereas the isomeric derivatives D-tagatose-6-phosphate (Tag-6P) and D-fructose-6-phosphate (Fru-6P) are inhibitors. Studies of catalytic efficiency (kcat/Km) reveal that the enzyme specificity is markedly in favor of Tag-1P as substrate. Importantly, we show in vivo that the transfer of the phosphate moiety from PEP to the B. licheniformis tagatose-specific enzyme II (EIITag) in E.coli is inefficient. The capability of the PTS general cytoplasmic components of B. subtilis, HPr and EI, to restore the phosphate transfer is demonstrated. PMID:26159072

  18. Mildly compromised tetrahydrobiopterin cofactor biosynthesis due to Pts variants leads to unusual body fat distribution and abdominal obesity in mice.

    PubMed

    Korner, Germaine; Scherer, Tanja; Adamsen, Dea; Rebuffat, Alexander; Crabtree, Mark; Rassi, Anahita; Scavelli, Rossana; Homma, Daigo; Ledermann, Birgit; Konrad, Daniel; Ichinose, Hiroshi; Wolfrum, Christian; Horsch, Marion; Rathkolb, Birgit; Klingenspor, Martin; Beckers, Johannes; Wolf, Eckhard; Gailus-Durner, Valérie; Fuchs, Helmut; Hrabě de Angelis, Martin; Blau, Nenad; Rozman, Jan; Thöny, Beat

    2016-03-01

    Tetrahydrobiopterin (BH4) is an essential cofactor for the aromatic amino acid hydroxylases, alkylglycerol monooxygenase, and nitric oxide synthases (NOS). Inborn errors of BH4 metabolism lead to severe insufficiency of brain monoamine neurotransmitters while augmentation of BH4 by supplementation or stimulation of its biosynthesis is thought to ameliorate endothelial NOS (eNOS) dysfunction, to protect from (cardio-) vascular disease and/or prevent obesity and development of the metabolic syndrome. We have previously reported that homozygous knock-out mice for the 6-pyruvolytetrahydropterin synthase (PTPS; Pts-ko/ko) mice with no BH4 biosynthesis die after birth. Here we generated a Pts-knock-in (Pts-ki) allele expressing the murine PTPS-p.Arg15Cys with low residual activity (15% of wild-type in vitro) and investigated homozygous (Pts-ki/ki) and compound heterozygous (Pts-ki/ko) mutants. All mice showed normal viability and depending on the severity of the Pts alleles exhibited up to 90% reduction of PTPS activity concomitant with neopterin elevation and mild reduction of total biopterin while blood L-phenylalanine and brain monoamine neurotransmitters were unaffected. Yet, adult mutant mice with compromised PTPS activity (i.e., Pts-ki/ko, Pts-ki/ki or Pts-ko/wt) had increased body weight and elevated intra-abdominal fat. Comprehensive phenotyping of Pts-ki/ki mice revealed alterations in energy metabolism with proportionally higher fat content but lower lean mass, and increased blood glucose and cholesterol. Transcriptome analysis indicated changes in glucose and lipid metabolism. Furthermore, differentially expressed genes associated with obesity, weight loss, hepatic steatosis, and insulin sensitivity were consistent with the observed phenotypic alterations. We conclude that reduced PTPS activity concomitant with mildly compromised BH4-biosynthesis leads to abnormal body fat distribution and abdominal obesity at least in mice. This study associates a novel

  19. Low-Complexity SLM and PTS Schemes for PAPR Reduction in OFDM Systems

    NASA Astrophysics Data System (ADS)

    Wang, Chin-Liang; Ouyang, Yuan; Hsu, Ming-Yen

    One major drawback of orthogonal frequency-division multiplexing is the high peak-to-average power ratio (PAPR) of the output signal. The selected mapping (SLM) and partial transmit sequences (PTS) methods are two promising techniques for PAPR reduction. However, to generate a set of candidate signals, these techniques need a bank of inverse fast Fourier transforms (IFFT's) and thus require high computational complexity. In this paper, we propose two low-complexity multiplication-free conversion processes to replace the IFFT's in the SLM method, where each conversion process for an N-point IFFT involves only 3N complex additions. Using these proposed conversions, we develop several new SLM schemes and a combined SLM & PTS method, in which at least half of the IFFT blocks are reduced. Computer simulation results show that, compared to the conventional methods, these new schemes have approximately the same PAPR reduction performance under the same number of candidate signals for transmission selection.

  20. Regulation of Streptococcus mutans PTS Bio by the transcriptional repressor NigR.

    PubMed

    Vujanac, M; Iyer, V S; Sengupta, M; Ajdic, D

    2015-08-01

    Streptococcus mutans is implicated in human dental caries, and the carbohydrate metabolism of this organism plays an important role in the formation of this disease. Carbohydrate transport and metabolism are essential for the survival of S. mutans in the oral cavity. It is known that a unique phosphoenolpyruvate-sugar phosphotransferase system PTS(B) (io) of S. mutans UA159 is expressed in sucrose-grown biofilms (Mol Oral Microbiol 28: 2013; 114). In this study we analyzed the transcriptional regulation of the operon (O(B) (io) ) encoding the PTS(B) (io) and showed that it was repressed by NigR, a LacI-like transcriptional regulator. Using electro-mobility shift assay, we described two operators to which NigR bound with different affinities. We also identified the transcriptional start site and showed that one of the operators overlaps with the promoter and presumably represses initiation of transcription. Mutational analyses revealed the key nucleotides in the operators required for high-affinity binding of NigR. PTS(B) (io) is expressed in S. mutans biofilms so understanding its regulation may provide improved strategies for caries treatment and prevention. PMID:25580872

  1. Assessing Safety of Pneumatic Tube System (PTS) for Patients with Very Low Hematologic Parameters

    PubMed Central

    Koroglu, Mustafa; Erkurt, Mehmet Ali; Kuku, Irfan; Kaya, Emin; Berber, Ilhami; Nizam, Ilknur; Yagar, Yavuz; Kayis, Seyit Ali

    2016-01-01

    Background Preventive interventions save lives during the process of chemotherapy for hematologic malignancies, when a hematology laboratory can ensure accurate results. The use of a pneumatic tube system (PTS) is associated with measurement errors and unnecessary transfusions. The aim of this study was to evaluate pre-analytical errors associated with transportation method (PTS versus hand-delivered) and to investigate whether there are unnecessary transfusion events in pancytopenia leukemia patients with very low hematological parameters. Material/Methods A total of 140 paired blood collections were performed for hemogram and biochemistry assays. Paired EDTA and serum gel blood samples were collected from 58 cases with acute leukemia on different days. For each pair, one sample was hand-delivered by a courier (Group 1) while the other sample was transported through a PTS (Group 2). Results The hand-delivered method showed that some platelet transfusions were unnecessary for different thrombocyte cut-off values. Calculated unnecessary platelet (PLT) transfusion ratios when using PTS (PLT <30×103/μL, 16.3%; PLT <25×103/μL, 16.4%; PLT <20×103/μL, 80.3%; PLT <15×103/μL, 48.6%; and PLT <10×103/μL, 150.0%) were found to be statistically significant (p=0.002, p=0.046, p<0.000, p=0.028, and p<0.000, respectively). In contrast, for RBC transfusion ratios, although the ratios were high in Group 2, we found no significant difference between the two groups; (HGB <8.0 g/dL, 23.3%; HGB <9.0 g/dL, 25.0%, HGB<10.0 g/dL, 19.3%) and (p=0.002, p=0.085, p<0.160, and p=0.235, respectively). Conclusions Although our results cannot be universally applied, physicians should be careful, skeptical, and suspicious of transfusion decisions in hematology clinics and consider potential analytical and pre-analytical errors in cases of severe cytopenia when using PTS. PMID:27097101

  2. Seryl-phosphorylated HPr regulates CcpA-independent carbon catabolite repression in conjunction with PTS permeases in Streptococcus mutans.

    PubMed

    Zeng, Lin; Burne, Robert A

    2010-03-01

    Carbohydrate catabolite repression (CCR) in Streptococcus mutans can be independent of catabolite control protein A (CcpA) and requires specific components of phosphoenolpyruvate-dependent sugar:phosphotransferase system (PTS) permeases. Here, the effects of various ptsH (HPr) and hprK (HPr kinase/phosphatase) mutations on growth and CCR were evaluated. An hprKV265F mutation, which enhanced Ser46 phosphorylation of HPr, inhibited growth on multiple PTS sugars. A ptsHS46A mutation reversed the effects of hprKV265F in most cases. A strain carrying a ptsHS46D mutation, which mimics HPr(Ser-P), presented with more severe growth defects than the hprKV265F mutant. The hprKV265F mutant enhanced CCR of the fruA and levD operons, a phenotype reversible by the ptsHS46A mutation. The effects of the hprKV265F mutation on fruA and levD expression were independent of CcpA, but dependent on ManL (IIAB(Man)) and, to a lesser extent, on FruI (IIABC(Fru)), in a carbohydrate-specific fashion. Expression of the Bacillus subtilis ptsG gene in the manL mutant did not restore CCR of the lev or fru operons. The hprKV265F mutation inhibited growth on cellobiose and lactose, but only the transcription of the cel operon was decreased. Thus, in S. mutans, serine-phosphorylated HPr functions in concert with particular PTS permeases to prioritize carbohydrate utilization by modulating sugar transport and transcription of catabolic operons. PMID:20487301

  3. PTS-Mediated Regulation of the Transcription Activator MtlR from Different Species: Surprising Differences despite Strong Sequence Conservation.

    PubMed

    Joyet, Philippe; Derkaoui, Meriem; Bouraoui, Houda; Deutscher, Josef

    2015-01-01

    The hexitol D-mannitol is transported by many bacteria via a phosphoenolpyruvate (PEP):carbohydrate phosphotransferase system (PTS). In most Firmicutes, the transcription activator MtlR controls the expression of the genes encoding the D-mannitol-specific PTS components and D-mannitol-1-P dehydrogenase. MtlR contains an N-terminal helix-turn-helix motif followed by an Mga-like domain, two PTS regulation domains (PRDs), an EIIB(Gat)- and an EIIA(Mtl)-like domain. The four regulatory domains are the target of phosphorylation by PTS components. Despite strong sequence conservation, the mechanisms controlling the activity of MtlR from Lactobacillus casei, Bacillus subtilis and Geobacillus stearothermophilus are quite different. Owing to the presence of a tyrosine in place of the second conserved histidine (His) in PRD2, L. casei MtlR is not phosphorylated by Enzyme I (EI) and HPr. When the corresponding His in PRD2 of MtlR from B. subtilis and G. stearothermophilus was replaced with alanine, the transcription regulator was no longer phosphorylated and remained inactive. Surprisingly, L. casei MtlR functions without phosphorylation in PRD2 because in a ptsI (EI) mutant MtlR is constitutively active. EI inactivation prevents not only phosphorylation of HPr, but also of the PTS(Mtl) components, which inactivate MtlR by phosphorylating its EIIB(Gat)- or EIIA(Mtl)-like domain. This explains the constitutive phenotype of the ptsI mutant. The absence of EIIB(Mtl)-mediated phosphorylation leads to induction of the L. caseimtl operon. This mechanism resembles mtlARFD induction in G. stearothermophilus, but differs from EIIA(Mtl)-mediated induction in B. subtilis. In contrast to B. subtilis MtlR, L. casei MtlR activation does not require sequestration to the membrane via the unphosphorylated EIIB(Mtl) domain. PMID:26159071

  4. Variable length adjacent partitioning for PTS based PAPR reduction of OFDM signal

    NASA Astrophysics Data System (ADS)

    Ibraheem, Zeyid T.; Rahman, Md. Mijanur; Yaakob, S. N.; Razalli, Mohammad Shahrazel; Kadhim, Rasim A.

    2015-05-01

    Peak-to-Average power ratio (PAPR) is a major drawback in OFDM communication. It leads the power amplifier into nonlinear region operation resulting into loss of data integrity. As such, there is a strong motivation to find techniques to reduce PAPR. Partial Transmit Sequence (PTS) is an attractive scheme for this purpose. Judicious partitioning the OFDM data frame into disjoint subsets is a pivotal component of any PTS scheme. Out of the existing partitioning techniques, adjacent partitioning is characterized by an attractive trade-off between cost and performance. With an aim of determining effects of length variability of adjacent partitions, we performed an investigation into the performances of a variable length adjacent partitioning (VL-AP) and fixed length adjacent partitioning in comparison with other partitioning schemes such as pseudorandom partitioning. Simulation results with different modulation and partitioning scenarios showed that fixed length adjacent partition had better performance compared to variable length adjacent partitioning. As expected, simulation results showed a slightly better performance of pseudorandom partitioning technique compared to fixed and variable adjacent partitioning schemes. However, as the pseudorandom technique incurs high computational complexities, adjacent partitioning schemes were still seen as favorable candidates for PAPR reduction.

  5. Variable length adjacent partitioning for PTS based PAPR reduction of OFDM signal

    SciTech Connect

    Ibraheem, Zeyid T.; Rahman, Md. Mijanur; Yaakob, S. N.; Razalli, Mohammad Shahrazel; Kadhim, Rasim A.

    2015-05-15

    Peak-to-Average power ratio (PAPR) is a major drawback in OFDM communication. It leads the power amplifier into nonlinear region operation resulting into loss of data integrity. As such, there is a strong motivation to find techniques to reduce PAPR. Partial Transmit Sequence (PTS) is an attractive scheme for this purpose. Judicious partitioning the OFDM data frame into disjoint subsets is a pivotal component of any PTS scheme. Out of the existing partitioning techniques, adjacent partitioning is characterized by an attractive trade-off between cost and performance. With an aim of determining effects of length variability of adjacent partitions, we performed an investigation into the performances of a variable length adjacent partitioning (VL-AP) and fixed length adjacent partitioning in comparison with other partitioning schemes such as pseudorandom partitioning. Simulation results with different modulation and partitioning scenarios showed that fixed length adjacent partition had better performance compared to variable length adjacent partitioning. As expected, simulation results showed a slightly better performance of pseudorandom partitioning technique compared to fixed and variable adjacent partitioning schemes. However, as the pseudorandom technique incurs high computational complexities, adjacent partitioning schemes were still seen as favorable candidates for PAPR reduction.

  6. Primary experimental results of wire-array Z-pinches on PTS

    SciTech Connect

    Huang, X. B. Zhou, S. T. Ren, X. D. Dan, J. K. Wang, K. L. Zhang, S. Q. Li, J. Xu, Q. Cai, H. C. Duan, S. C. Ouyang, K. Chen, G. H. Ji, C. Wang, M. Feng, S. P. Yang, L. B. Xie, W. P. Deng, J. J.

    2014-12-15

    The Primary Test Stand (PTS) developed at the China Academy of Engineering Physics is a multiterawatt pulsed power driver, which can deliver a ∼10 MA, 70 ns rise-time (10%-90%) current to a short circuit load and has important applications in Z-pinch driven inertial confinement fusion and high energy density physics. In this paper, primary results of tungsten wire-array Z-pinch experiments on PTS are presented. The load geometries investigated include 15-mm-tall cylindrical single and nested arrays with diameter ranging from 14.4-26.4 mm, and consisting of 132∼276 tungsten wires with 5∼10 μm in diameter. Multiple diagnostics were fielded to determine the characteristics of x-ray radiations and to obtain self-emitting images of imploding plasmas. X-ray power up to 80 TW with ∼3 ns FWMH is achieved by using nested wire arrays. The total x-ray energy exceeds 500 kJ and the peak radiation temperature is about 150 eV. Typical velocity of imploding plasmas goes around 3∼5×10{sup 7} cm/s and the radial convergence ratio is between 10 and 20.

  7. Glucose Transporter Mutants of Escherichia coli K-12 with Changes in Substrate Recognition of IICBGlc and Induction Behavior of the ptsG Gene

    PubMed Central

    Zeppenfeld, Tim; Larisch, Christina; Lengeler, Joseph W.; Jahreis, Knut

    2000-01-01

    In Escherichia coli K-12, the major glucose transporter with a central role in carbon catabolite repression and in inducer exclusion is the phosphoenolpyruvate-dependent glucose:phosphotransferase system (PTS). Its membrane-bound subunit, IICBGlc, is encoded by the gene ptsG; its soluble domain, IIAGlc, is encoded by crr, which is a member of the pts operon. The system is inducible by d-glucose and, to a lesser degree, by l-sorbose. The regulation of ptsG transcription was analyzed by testing the induction of IICBGlc transporter activity and of a single-copy Φ(ptsGop-lacZ) fusion. Among mutations found to affect directly ptsG expression were those altering the activity of adenylate cyclase (cyaA), the repressor DgsA (dgsA; also called Mlc), the general PTS proteins enzyme I (ptsI) and histidine carrier protein HPr (ptsH), and the IIAGlc and IIBGlc domains, as well as several authentic and newly isolated UmgC mutations. The latter, originally thought to map in the repressor gene umgC outside the ptsG locus, were found to represent ptsG alleles. These affected invariably the substrate specificity of the IICBGlc domain, thus allowing efficient transport and phosphorylation of substrates normally transported very poorly or not at all by this PTS. Simultaneously, all of these substrates became inducers for ptsG. From the analysis of the mutants, from cis-trans dominance tests, and from the identification of the amino acid residues mutated in the UmgC mutants, a new regulatory mechanism involved in ptsG induction is postulated. According to this model, the phosphorylation state of IIBGlc modulates IICGlc which, directly or indirectly, controls the repressor DgsA and hence ptsG expression. By the same mechanism, glucose uptake and phosphorylation also control the expression of the pts operon and probably of all operons controlled by the repressor DgsA. PMID:10913077

  8. Reducing PAPR of optical OFDM system based on PTS and companding joint algorithm

    NASA Astrophysics Data System (ADS)

    Jia, Yangjing; Li, Ping; Lei, Dongming; Chen, Ailin; Wang, Jinpeng; Zou, Nianyu

    2015-10-01

    Optical orthogonal frequency division multiplexing (OFDM) system combines the advantages of both wireless OFDM and optical fiber technology, thus has high spectral efficiency and can effectively resist polarization mode dispersion and chromatic dispersion in fiber link. However, high peak-to-average power ratio (PAPR) is one of the important shortcomings of optical OFDM system, which requires not only amplifiers with a greater dynamic range, but also leads to serious fiber nonlinear effect. So how to reduce PAPR of optical OFDM system is a crucial issue. This work, aiming to reduce PAPR and improving system BER, analyzes suppression technology of PAPR based on optical OFDM system. Firstly, to improve BER, we utilize Partial Transmit Sequence (PTS) algorithm which introduces phase factors b(v) multiplying IFFT converted signals and searches a b(v) which will make PAPR minimum. But this method needs much calculation. Then we exploit companding which can compress amplitude of big OFDM signals and expand small signals. Secondly, simulating the two algorithms respectively and finding two algorithms can suppress PAPR, but the effect has room for improvement. Therefore, an implementation of PTS and companding joint algorithm is proposed, then simulating this method and adding it into optical OFDM system. A system was set up, fiber length setting as 10km, utilizing a MZM modulator and a distributed feedback laser, taking 4QAM and 512points IFFT. The results show that, joint algorithm can reduce PAPR from about 12dB to 8dB, improving the problem of high PAPR, constellation convergence, enhances optical OFDM system transmission performance.

  9. Molecular Recognition of PTS-1 Cargo Proteins by Pex5p: Implications for Protein Mistargeting in Primary Hyperoxaluria

    PubMed Central

    Mesa-Torres, Noel; Tomic, Nenad; Albert, Armando; Salido, Eduardo; Pey, Angel L.

    2015-01-01

    Peroxisomal biogenesis and function critically depends on the import of cytosolic proteins carrying a PTS1 sequence into this organelle upon interaction with the peroxin Pex5p. Recent structural studies have provided important insights into the molecular recognition of cargo proteins by Pex5p. Peroxisomal import is a key feature in the pathogenesis of primary hyperoxaluria type 1 (PH1), where alanine:glyoxylate aminotransferase (AGT) undergoes mitochondrial mistargeting in about a third of patients. Here, we study the molecular recognition of PTS1 cargo proteins by Pex5p using oligopeptides and AGT variants bearing different natural PTS1 sequences, and employing an array of biophysical, computational and cell biology techniques. Changes in affinity for Pex5p (spanning over 3–4 orders of magnitude) reflect different thermodynamic signatures, but overall bury similar amounts of molecular surface. Structure/energetic analyses provide information on the contribution of ancillary regions and the conformational changes induced in Pex5p and the PTS1 cargo upon complex formation. Pex5p stability in vitro is enhanced upon cargo binding according to their binding affinities. Moreover, we provide evidence that the rational modulation of the AGT: Pex5p binding affinity might be useful tools to investigate mistargeting and misfolding in PH1 by pulling the folding equilibria towards the native and peroxisomal import competent state. PMID:25689234

  10. New PAPR Reduction in an OFDM System Using Hybrid of PTS-CAPPR Methods with GA Coded Side Information Technique

    NASA Astrophysics Data System (ADS)

    Pradabpet, Chusit; Yoshizawa, Shingo; Miyanaga, Yoshikazu; Dejhan, Kobchai

    In this paper, we propose a new PAPR reduction by using the hybrid of partial transmit sequences (PTS) and cascade adaptive peak power reduction (CAPPR) methods with side information (SI) technique coded by genetic algorithm (GA). These methods are used in an Orthogonal Frequency Division Multiplexing (OFDM) system. The OFDM employs orthogonal sub-carriers for data modulation. These sub-carriers unexpectedly present a large peak to average power ratio (PAPR) in some cases. A proposed reduction method realizes both the advantages of PTS and CAPPR at the same time. In order to obtain the optimum condition on PTS for PAPR reduction, a quite large calculation cost is demanded and thus it is impossible to obtain the optimum PTS in a short time. In the proposed method, by using the pseudo-optimum condition based on a GA coded SI technique, the total calculation cost becomes drastically reduced. In simulation results, the proposed method shows the improvement on PAPR and also reveals the high performance on bit error rate (BER) of an OFDM system.

  11. New PAPR Reduction in OFDM System Using Hybrid of PTS-APPR Methods with Coded Side Information Technique

    NASA Astrophysics Data System (ADS)

    Pradabpet, Chusit; Yoshizawa, Shingo; Miyanaga, Yoshikazu; Dejhan, Kobchai

    In this paper, we propose a new PAPR reduction by using the hybrid of a partial transmit sequences (PTS) and an adaptive peak power reduction (APPR) methods with coded side information (SI) technique. These methods are used in an Orthogonal Frequency Division Multiplexing (OFDM) system. The OFDM employs orthogonal sub-carriers for data modulation. These sub-carriers unexpectedly present a large Peak to Average Power Ratio (PAPR) in some cases. In order to reduce PAPR, the sequence of input data is rearranged by PTS. The APPR method is also used to controls the peak level of modulation signals by an adaptive algorithm. A proposed reduction method consists of these two methods and realizes both advantages at the same time. In order to make the optimum condition on PTS for PAPR reduction, a quite large calculation cost must be demanded and thus it is impossible to obtain the optimum PTS. In the proposed method, by using the pseudo-optimum condition with a coded SI technique, the total calculation cost becomes drastically reduced. In simulation results, the proposed method shows the improvement on PAPR and also reveals the high performance on bit error rate (BER) of an OFDM system.

  12. Family and Individual Factors Associated with Substance Involvement and PTS Symptoms among Adolescents in Greater New Orleans after Hurricane Katrina

    ERIC Educational Resources Information Center

    Rowe, Cynthia L.; La Greca, Annette M.; Alexandersson, Anders

    2010-01-01

    Objective: This study examined the influence of hurricane impact as well as family and individual risk factors on posttraumatic stress (PTS) symptoms and substance involvement among clinically referred adolescents affected by Hurricane Katrina. Method: A total of 80 adolescents (87% male; 13-17 years old; mean age = 15.6 years; 38% minorities) and…

  13. Comparison of Tc-99m DTPA aerosol with radioactive gas ventilation imaging in patients (pts) with suspected pulmonary embolism (PE)

    SciTech Connect

    Alderson, P.O.; Kroop, S.A.; Biello, D.R.; Siegel, B.A.; Gottschalk, A.; Hoffer, P.B.; Ramanna, L.; Waxman, A.D.

    1984-01-01

    The utility of Tc-99m labeled DTPA aerosol (A) as a ventilation agent was compared to that of Xe-133 (Xe) or Kr-81m (Kr) gases in a series of 100 pts (age range 20-83, 53% women) undergoing ventilation-perfusion (V-P) imaging for suspected PE. The majority of pts had A and Xe studies in conjunction with P scans; 26 had A and Kr studies. All A studies were comprised of multiple 100K ct views performed prior to P scanning. Conventional Xe or Kr studies were then performed in conjunction with a multiview P scan. The studies were later reviewed by four independent readers who evaluated 100 V-P studies (100 A-P pairs, 100 gas-P pairs) and the accompanying chest radiographs and determined the probability of PE as none, low, high, or nondiagnostic (NDX). The A scans showed central hot spots in 27% of pts, but poor peripheral penetration in only 5%. Prominent lower lobe deposition was seen in 19 of the 66 pts who inhaled A upright, but in none who inhaled in the supine position. The A-P and gas-P scans were either both diagnostic or both NDX 82% of the time. There were 77% agreement between probability categories for A-P and Kr-P studies, and 74% agreement with Xe-P. These results were better than the inter-observer agreement for gas-P studies alone. Angiography revealed that 3 A-P studies were true negatives, 3 were true positives (pos), and one was a false pos (also pos by gas-P). The results suggest that commercially available DTPA aerosols provide comparable results to gas-P studies in pts with suspected PE.

  14. Tysnd1 Deficiency in Mice Interferes with the Peroxisomal Localization of PTS2 Enzymes, Causing Lipid Metabolic Abnormalities and Male Infertility

    PubMed Central

    Mizuno, Yumi; Ninomiya, Yuichi; Nakachi, Yutaka; Iseki, Mioko; Iwasa, Hiroyasu; Akita, Masumi; Tsukui, Tohru; Shimozawa, Nobuyuki; Ito, Chizuru; Toshimori, Kiyotaka; Nishimukai, Megumi; Hara, Hiroshi; Maeba, Ryouta; Okazaki, Tomoki; Alodaib, Ali Nasser Ali; Amoudi, Mohammed Al; Jacob, Minnie; Alkuraya, Fowzan S.; Horai, Yasushi; Watanabe, Mitsuhiro; Motegi, Hiromi; Wakana, Shigeharu; Noda, Tetsuo; Kurochkin, Igor V.; Mizuno, Yosuke; Schönbach, Christian; Okazaki, Yasushi

    2013-01-01

    Peroxisomes are subcellular organelles involved in lipid metabolic processes, including those of very-long-chain fatty acids and branched-chain fatty acids, among others. Peroxisome matrix proteins are synthesized in the cytoplasm. Targeting signals (PTS or peroxisomal targeting signal) at the C-terminus (PTS1) or N-terminus (PTS2) of peroxisomal matrix proteins mediate their import into the organelle. In the case of PTS2-containing proteins, the PTS2 signal is cleaved from the protein when transported into peroxisomes. The functional mechanism of PTS2 processing, however, is poorly understood. Previously we identified Tysnd1 (Trypsin domain containing 1) and biochemically characterized it as a peroxisomal cysteine endopeptidase that directly processes PTS2-containing prethiolase Acaa1 and PTS1-containing Acox1, Hsd17b4, and ScpX. The latter three enzymes are crucial components of the very-long-chain fatty acids β-oxidation pathway. To clarify the in vivo functions and physiological role of Tysnd1, we analyzed the phenotype of Tysnd1−/− mice. Male Tysnd1−/− mice are infertile, and the epididymal sperms lack the acrosomal cap. These phenotypic features are most likely the result of changes in the molecular species composition of choline and ethanolamine plasmalogens. Tysnd1−/− mice also developed liver dysfunctions when the phytanic acid precursor phytol was orally administered. Phyh and Agps are known PTS2-containing proteins, but were identified as novel Tysnd1 substrates. Loss of Tysnd1 interferes with the peroxisomal localization of Acaa1, Phyh, and Agps, which might cause the mild Zellweger syndrome spectrum-resembling phenotypes. Our data established that peroxisomal processing protease Tysnd1 is necessary to mediate the physiological functions of PTS2-containing substrates. PMID:23459139

  15. A probabilistic approach to the evaluation of the PTS (pressurized thermal shock) issue

    SciTech Connect

    Cheverton, R.D.; Selby, D.L.

    1990-01-01

    The pressurized-thermal-shock (PTS) issue is concerned with the possibility of failure of pressurized-water-reactor (PWR) pressure vessels under a very specific set of conditions. These conditions include: (1) the occurrence of reactor transients that subject the vessel to severe thermal shock as well as the normal pressure loading, (2) the existence of sharp, crack-like defects (flaws) at the inner surface of the vessel wall, and (3) high enough fast neutron fluence and concentrations of copper and nickel in the vessel wall to result in a extensive radiation-included reduction in the fracture toughness of the vessel material. Under these conditions, the mechanism for vessel failure involves propagation of the flaws through the vessel wall, in which case adequate containment of coolant for the core might not be possible. The portion of the vessel of concern is the so-called beltline region because, it is directly opposite the core (high influence rate), it is adjacent to the coolant downcomer (potential for thermal shock), and coolant leakage in this area would tend to uncover the core. This document discusses the behavior of flaws in reactor pressure vessels under pressure and thermal-shock loading conditions.

  16. Characterization of injection wells in a fractured reservoir using PTS logs, Steamboat Hills Geothermal Field, Nevada, USA

    SciTech Connect

    Goranson, Colin; Combs, Jim

    1995-01-26

    The Steamboat Hills Geothermal Field in northwestern Nevada, about 15 km south of Reno, is a shallow (150m to 825m) moderate temperature (155 C to 168 C) liquid-dominated geothermal reservoir situated in highly-fractured granodiorite. Three injection wells were drilled and completed in granodiorite to dispose of spent geothermal fluids from the Steamboat II and III power plants (a 30 MW air-cooled binary-type facility). Injection wells were targeted to depths below 300m to inject spent fluids below producing fractures. First, quasi-static downhole pressure-temperature-spinner (PTS) logs were obtained. Then, the three wells were injection-tested using fluids between 80 C and 106 C at rates from 70 kg/s to 200 kg/s. PTS logs were run both up and down the wells during these injection tests. These PTS surveys have delineated the subsurface fracture zones which will accept fluid. The relative injectivity of the wells was also established. Shut-in interzonal flow within the wells was identified and characterized.

  17. NMR analysis of biodiesel

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Biodiesel is usually analyzed by the various methods called for in standards such as ASTM D6751 and EN 14214. Nuclear magnetic resonance (NMR) is not one of these methods. However, NMR, with 1H-NMR commonly applied, can be useful in a variety of applications related to biodiesel. These include monit...

  18. LOCAD-PTS: Operation of a New System for Microbial Monitoring Aboard the International Space Station (ISS)

    NASA Technical Reports Server (NTRS)

    Maule, J.; Wainwright, N.; Steele, A.; Gunter, D.; Flores, G.; Effinger, M.; Danibm N,; Wells, M.; Williams, S.; Morris, H.; Monaco, L.

    2008-01-01

    Microorganisms within the space stations Salyut, Mir and the International Space Station (ISS), have traditionally been monitored with culture-based techniques. These techniques involve growing environmental samples (cabin water, air or surfaces) on agar-type media for several days, followed by visualization of resulting colonies; and return of samples to Earth for ground-based analysis. This approach has provided a wealth of useful data and enhanced our understanding of the microbial ecology within space stations. However, the approach is also limited by the following: i) More than 95% microorganisms in the environment cannot grow on conventional growth media; ii) Significant time lags occur between onboard sampling and colony visualization (3-5 days) and ground-based analysis (as long as several months); iii) Colonies are often difficult to visualize due to condensation within contact slide media plates; and iv) Techniques involve growth of potentially harmful microorganisms, which must then be disposed of safely. This report describes the operation of a new culture-independent technique onboard the ISS for rapid analysis (within minutes) of endotoxin and -1, 3-glucan, found in the cell walls of gram-negative bacteria and fungi, respectively. This technique involves analysis of environmental samples with the Limulus Amebocyte Lysate (LAL) assay in a handheld device. This handheld device and sampling system is known as the Lab-On-a-Chip Application Development Portable Test System (LOCAD-PTS). A poster will be presented that describes a comparative study between LOCAD-PTS analysis and existing culture-based methods onboard the ISS; together with an exploratory survey of surface endotoxin throughout the ISS. It is concluded that while a general correlation between LOCAD-PTS and traditional culture-based methods should not necessarily be expected, a combinatorial approach can be adopted where both sets of data are used together to generate a more complete story of

  19. Transformation of a metal-organic framework from the NbO to PtS net.

    PubMed

    Chen, Banglin; Ockwig, Nathan W; Fronczek, Frank R; Contreras, Damacio S; Yaghi, Omar M

    2005-01-24

    Two metal-organic frameworks (MOFs), MOF-501 and MOF-502, respectively, formulated as Co(2)(BPTC)(H(2)O)(5).G(x) and Co(2)(BPTC)(H(2)O)(DMF)(2).G(x) (BPTC = 3,3',5,5'-biphenyltetracarboxylate; G = guest molecules), have been synthesized and structurally characterized, and their topologies were found to be based on the NbO (MOF-501) and PtS (MOF-502) nets. Heating MOF-501 in solution results in the more thermodynamically favored MOF-502. PMID:15651861

  20. Two dimensional NMR spectroscopy

    SciTech Connect

    Schram, J.; Bellama, J.M.

    1988-01-01

    Two dimensional NMR represents a significant achievement in the continuing effort to increase solution in NMR spectroscopy. This book explains the fundamentals of this new technique and its analytical applications. It presents the necessary information, in pictorial form, for reading the ''2D NMR,'' and enables the practicing chemist to solve problems and run experiments on a commercial spectrometer by using the software provided by the manufacturer.

  1. Fully 3D Particle-in-Cell Simulation of Double Post-Hole Convolute on PTS Facility

    NASA Astrophysics Data System (ADS)

    Zhao, Hailong; Dong, Ye; Zhou, Haijing; Zou, Wenkang; Institute of Fluid Physics Collaboration; Institute of Applied Physics; Computational Mathematics Collaboration

    2015-11-01

    In order to get better understand of energy transforming and converging process during High Energy Density Physics (HEDP) experiments, fully 3D particle-in-cell (PIC) simulation code NEPTUNE3D was used to provide numerical approach towards parameters which could hardly be acquired through diagnostics. Cubic region (34cm × 34cm × 18cm) including the double post-hole convolute (DPHC) on the primary test stand (PTS) facility was chosen to perform a series of fully 3D PIC simulations, calculating ability of codes were tested and preliminary simulation results about DPHC on PTS facility were discussed. Taking advantages of 3D simulation codes and large-scale parallel computation, massive data (~ 250GB) could be acquired in less than 5 hours and clear process of current transforming and electron emission in DPHC were demonstrated with the help of visualization tools. Cold-chamber tests were performed during which only cathode electron emission was considered without temperature rise or ion emission, current loss efficiency was estimated to be 0.46% ~ 0.48% by comparisons between output magnetic field profiles with or without electron emission. Project supported by the National Natural Science Foundation of China (Grant No. 11205145, 11305015, 11475155).

  2. Lectures on pulsed NMR

    SciTech Connect

    Pines, A.

    1988-08-01

    These lectures discuss some recent developments in pulsed NMR, emphasizing fundamental principles with selected illustrative applications. Major topics covered include multiple-quantum spectroscopy, spin decoupling, the interaction of spins with a quantized field, adiabatic rapid passage, spin temperature and statistics of cross-polarization, coherent averaging, and zero field NMR. 32 refs., 56 figs.

  3. Lectures on pulsed NMR

    SciTech Connect

    Pines, A.

    1986-09-01

    These lectures discuss some recent developments in pulsed NMR, emphasizing fundamental principles with selected illustrative applications. Major topics covered include multiple-quantum spectroscopy, spin decoupling, the interaction of spins with a quantized field, adiabatic rapid passage, spin temperature and statistics of cross-polarization, coherent averaging, and zero field NMR. 55 figs.

  4. NMR logging apparatus

    DOEpatents

    Walsh, David O; Turner, Peter

    2014-05-27

    Technologies including NMR logging apparatus and methods are disclosed. Example NMR logging apparatus may include surface instrumentation and one or more downhole probes configured to fit within an earth borehole. The surface instrumentation may comprise a power amplifier, which may be coupled to the downhole probes via one or more transmission lines, and a controller configured to cause the power amplifier to generate a NMR activating pulse or sequence of pulses. Impedance matching means may be configured to match an output impedance of the power amplifier through a transmission line to a load impedance of a downhole probe. Methods may include deploying the various elements of disclosed NMR logging apparatus and using the apparatus to perform NMR measurements.

  5. Silver and Gold NMR

    PubMed Central

    Zangger, Klaus

    1999-01-01

    Silver and gold, together with copper, form the transition metal group IB elements in the periodic table and possess very different nuclear magnetic resonance (NMR) spectroscopic properties. While there is only one gold isotope (197Au), which has a spin of 3/2 and therefore a quadrupole moment, silver occurs in two isotopic forms (109Ag and 109Au), both of which have a spin 1/2 and similar NMR spectroscopic properties. The unfavorable properties of gold have prevented its NMR spectroscopic investigation thus far. On the other hand, there are several reports of silver NMR. However, the low sensitivity of silver, combined with its long relaxation times have rendered the direct detection of silver possible only with concentrations greater than a few tenth molar. Reviewed here are the general limitations of silver NMR and some techniques to partially overcome these limitations, as well as a summary of currently available chemical shift and scalar coupling data on 109Ag. PMID:18475898

  6. Synbiotic impact of tagatose on viability of Lactobacillus rhamnosus strain GG mediated by the phosphotransferase system (PTS).

    PubMed

    Koh, Ji Hoon; Choi, Seung Hye; Park, Seung Won; Choi, Nag-Jin; Kim, Younghoon; Kim, Sae Hun

    2013-10-01

    Synbiotics, the combination of prebiotics and probiotics, has been shown to produce synergistic effects that promote gastrointestinal well-being of host. Tagatose is a low calorie food ingredient with putative health-promoting benefits. Herein, we investigated its synbiotic impact on the viability of Lactobacillus casei 01 and Lactobacillus rhamnosus strain GG and the potential mechanism involved. Tagatose, as a synbiotic substrate, enhanced the growth of L. casei 01 and L. rhamnosus strain GG compared to other prebiotics. Other gut-indigenous such as Clostridium spp. readily utilized fructooligosaccharide (FOS), the most widely used functional prebiotics, but not tagatose. Additionally, tagatose enhanced probiotic functions of L. casei 01 and L. rhamnosus strain GG by reinforcing their attachment on HT-29 intestine epithelial cells and enhancing their cholesterol-lowering activities. Whole transcriptome study and quantitative real-time polymerase chain reaction (qRT-PCR) test showed that the presence of tagatose in L. rhamnosus strain GG caused induction of a large number of genes associated with carbohydrate metabolism including the phosphotransferase system (PTS). Collectively, these results indicate the tagatose enhanced the growth of L. casei 01 and L. rhamnosus strain GG and their probiotic activities by activating tagatose-associated PTS networks. Importantly, this study highlights the potential application of tagatose and L. casei 01 and/or L. rhamnosus strain GG as a synbiotic partner in functional dairy foods (i.e. yogurt and cheese) and therapeutic dietary supplements. PMID:23764214

  7. SOLA-PTS: a transient, three-dimensional algorithm for fluid-thermal mixing and wall heat transfer in complex geometries

    SciTech Connect

    Daly, B.J.; Torrey, M.D.

    1984-07-01

    The SOLA-PTS computer code has been developed to analyze fluid-thermal mixing in the cold legs and downcomer of pressurized water reactors in support of the pressurized thermal shock study. SOLA-PTS is a transient, three-dimensional code with the capability of resolving complex geometries using variable cell noding in the three coordinate directions. The computational procedure is second-order accurate and utilizes a state-of-the-art iteration method that allows rapid convergence to an accurate solution for the pressure field. Two different turbulence models are used in the code, a two-equation k-epsilon model that is used in the cold leg pipe away from the HPI inlet and a three-equation k-epsilon-T'/sup 2/ model for use near the HPI inlet and in the downcomer. The physical modeling and the numerical procedure used in SOLA-PTS are described in this report. Applications of the method to two Creare 1/5th-scale experiments are also presented. Two appendices are included which provides a comparison of the two- and three-equation turbulence models, and instructions for setting up and running a problem with SOLA-PTS.

  8. A Hybrid Peptide PTS that Facilitates Transmembrane Delivery and Its Application for the Rapid In vivo Imaging via Near-Infrared Fluorescence Imaging

    PubMed Central

    Yan, Xuejiao; Wu, Guoqiu; Qu, Qingrong; Fan, Xiaobo; Xu, Xudong; Liu, Naifeng

    2016-01-01

    Background and purpose: Intravital imaging provides invaluable readouts for clinical diagnoses and therapies and shows great potential in the design of individualized drug dosage regimes. Ts is a mammalian free cell membrane-penetrating peptide. This study aimed to introduce a novel approach to the design of a cancer-selective peptide on the basis of a membrane-penetrating peptide and to explore its potential as a carrier of medical substances. Experimental approach:Ts was linked with a αvβ3-binding peptide P1c to create a hybrid referred to as PTS. The hybrid was labeled with an FITC or Cy5.5 as an imaging indicator to evaluate its in vitro and in vivo bioactivity. Key results:Hemolysis tests proved that in comparison with Ts, PTS caused similar or even less leakage of human erythrocytes at concentrations of up to 1 mmol/L. Flow cytometry assay and confocal microscopy demonstrated the following. (1) P1c alone could target and mostly halt at the cancer cell membrane. (2) Ts alone could not bind to the membrane sufficiently. (3) P1c greatly enhanced the binding affinity of PTS with MDA-MB-231 breast cancer cells that upregulated αvβ3. (4) Ts conferred PTS with the ability to traverse a cell membrane and thus facilitate the transmembrane delivery of imaging probes. In vivo near-infrared fluorescence (NIRF) imaging demonstrated that the imaging probes were rapidly concentrated in a MDA-MB-231 tumor tissue within 1 h after intravenous injection. Conclusions and implications:PTS exhibited the capability of targeting specific tumors and greatly facilitating the transmembrane delivery of imaging probes. PMID:27014065

  9. NMR imaging microscopy

    SciTech Connect

    Not Available

    1986-10-01

    In the past several years, proton nuclear magnetic resonance (NMR) imaging has become an established technique in diagnostic medicine and biomedical research. Although much of the work in this field has been directed toward development of whole-body imagers, James Aguayo, Stephen Blackband, and Joseph Schoeninger of the Johns Hopkins University School of Medicine working with Markus Hintermann and Mark Mattingly of Bruker Medical Instruments, recently developed a small-bore NMR microscope with sufficient resolution to image a single African clawed toad cell (Nature 1986, 322, 190-91). This improved resolution should lead to increased use of NMR imaging for chemical, as well as biological or physiological, applications. The future of NMR microscopy, like that of many other newly emerging techniques, is ripe with possibilities. Because of its high cost, however, it is likely to remain primarily a research tool for some time. ''It's like having a camera,'' says Smith. ''You've got a way to look at things at very fine levels, and people are going to find lots of uses for it. But it is a very expensive technique - it costs $100,000 to add imaging capability once you have a high-resolution NMR, which itself is at least a $300,000 instrument. If it can answer even a few questions that can't be answered any other way, though, it may be well worth the cost.''

  10. Dual Species NMR Oscillator

    NASA Astrophysics Data System (ADS)

    Weber, Joshua; Korver, Anna; Thrasher, Daniel; Walker, Thad

    2016-05-01

    We present progress towards a dual species nuclear magnetic oscillator using synchronous spin exchange optical pumping. By applying the bias field as a sequence of alkali 2 π pulses, we generate alkali polarization transverse to the bias field. The alkali polarization is then modulated at the noble gas resonance so that through spin exchange collisions the noble gas becomes polarized. This novel method of NMR suppresses the alkali field frequency shift by at least a factor of 2500 as compared to longitudinal NMR. We will present details of the apparatus and measurements of dual species co-magnetometry using this method. Research supported by the NSF and Northrop-Grumman Corp.

  11. The permanent electric dipole moment of PtO, PtS, PtN, and PtC

    SciTech Connect

    Steimle, T.C.; Jung, K.Y.; Li, B.

    1995-08-01

    The permanent electric dipole moments of the ground, and the low-lying excited electronic states of platinum monocarbide, PtC, platinum monoxide, PtO, and platinum monosulfide, PtS, were measured using a molecular beam optical Stark spectroscopic scheme. The determined values were (in Debye): PtO({ital X} {sup 3}{Sigma}{sup {minus}}) 2.77(2); PtO({ital A} {sup 1}{Sigma}{sup +}) 1.15(4); PtS[{ital X}({Omega}=0)] 1.78(2); PtS[{ital B}({Omega}=0)] 0.54(6); PtC({ital X} {sup 1}{Sigma}{sup +}) 0.99(5); and PtC({ital A} {sup 1}{Pi}) 2.454(3). These results, along with the previous results for PtN({ital X} {sup 2}{Pi}{sub 1/2}) 1.977(9); PtN({ital d} {sup 4}{Pi}{sub 1/2}) 1.05(9) [J. Chem. Phys. {bold 102}, 643 (1995)], are used as a basis for a discussion of the nature of the electronic states. {copyright} {ital 1995} {ital American} {ital Institute} {ital of} {ital Physics}.

  12. Review of thermal-hydraulic calculations for Calvert Cliffs and H. B. Robinson PTS study. [Pressurized thermal shock

    SciTech Connect

    Jo, J.H.; Yuelys-Miksis, C.; Rohatgi, U.S.

    1984-01-01

    Thermal-hydraulic transient calculations performed by LANL using the TRAC-PF1 code and by INEL using the RELAP5 code for the USNRC pressurized thermal shock (PTS) study of the Calvert Cliffs and H.B. Robinson Nuclear Power Plants have been reviewed at BNL including the input decks and steady state calculations. Furthermore, six transients for each plant have been selected for the in-depth review. Simple hand calculations based on the mass and energy balances of the entire reactor system, have been performed to predict the temperature and pressure of the reactor system, and the results have been compared with those obtained by the code calculation. In general, the temperatures and pressures of the primary system calculated by the codes have been very reasonable. The secondary pressures calculated by TRAC appear to indicate that the codes have some difficulty with the condensation model and further work is needed to assess the code calculation of the U-tube steam generator pressure when the cold auxiliary feedwater is introduced to the steam generator. However, it is not expected that this uncertainty would affect the transient calculations significantly.

  13. Screening proteins for NMR suitability

    PubMed Central

    Yee, Adelinda A.; Semesi, Anthony; Garcia, Maite; Arrowsmith, Cheryl H.

    2014-01-01

    Summary NMR spectroscopy is an invaluable tool in structural genomics. Identification of protein samples that are amenable to structure determination by NMR spectroscopy requires efficient screening. Here, we describe how we prepare multiple samples in parallel and screen by NMR. The method described here is applicable to large structural genomics projects but can easily be scaled down for application to small structural biology projects since all the equipments used are those commonly found in any NMR structural biology laboratory. PMID:24590717

  14. Modern NMR Spectroscopy.

    ERIC Educational Resources Information Center

    Jelinski, Lynn W.

    1984-01-01

    Discusses direct chemical information that can be obtained from modern nuclear magnetic resonance (NMR) methods, concentrating on the types of problems that can be solved. Shows how selected methods provide information about polymers, bipolymers, biochemistry, small organic molecules, inorganic compounds, and compounds oriented in a magnetic…

  15. Enantiodiscrimination by NMR spectroscopy.

    PubMed

    Uccello-Barretta, Gloria; Balzano, Federica; Salvadori, Piero

    2006-01-01

    The analysis of enantiorecognition processes involves the detection of enantiomeric species as well as the study of chiral discrimination mechanisms. In both fields Nuclear Magnetic Resonance (NMR) spectroscopy plays a fundamental role, providing several tools, based on the use of suitable chiral auxiliaries, for observing distinct signals of enantiomers and for investigating the complexation phenomena involved in enantiodiscrimination processes. PMID:17100610

  16. Diversity of Streptococcus salivarius ptsH Mutants That Can Be Isolated in the Presence of 2-Deoxyglucose and Galactose and Characterization of Two Mutants Synthesizing Reduced Levels of HPr, a Phosphocarrier of the Phosphoenolpyruvate:Sugar Phosphotransferase System

    PubMed Central

    Thomas, Suzanne; Brochu, Denis; Vadeboncoeur, Christian

    2001-01-01

    In streptococci, HPr, a phosphocarrier of the phosphoenolpyruvate:sugar phosphotransferase transport system (PTS), undergoes multiple posttranslational chemical modifications resulting in the formation of HPr(His∼P), HPr(Ser-P), and HPr(Ser-P)(His∼P), whose cellular concentrations vary with growth conditions. Distinct physiological functions are associated with specific forms of HPr. We do not know, however, the cellular thresholds below which these forms become unable to fulfill their functions and to what extent modifications in the cellular concentrations of the different forms of HPr modify cellular physiology. In this study, we present a glimpse of the diversity of Streptococcus salivarius ptsH mutants that can be isolated by positive selection on a solid medium containing 2-deoxyglucose and galactose and identify 13 amino acids that are essential for HPr to properly accomplish its physiological functions. We also report the characterization of two S. salivarius mutants that produced approximately two- and threefoldless HPr and enzyme I (EI) respectively. The data indicated that (i) a reduction in the synthesis of HPr due to a mutation in the Shine-Dalgarno sequence of ptsH reduced ptsI expression; (ii) a threefold reduction in EI and HPr cellular levels did not affect PTS transport capacity; (iii) a twofold reduction in HPr synthesis was sufficient to reduce the rate at which cells metabolized PTS sugars, increase generation times on PTS sugars and to a lesser extent on non-PTS sugars, and impede the exclusion of non-PTS sugars by PTS sugars; (iv) a threefold reduction in HPr synthesis caused a strong derepression of the genes coding for α-galactosidase, β-galactosidase, and galactokinase when the cells were grown at the expense of a PTS sugar but did not affect the synthesis of α-galactosidase when cells were grown at the expense of lactose, a noninducing non-PTS sugar; and (v) no correlation was found between the magnitude of enzyme derepression and

  17. Maltose Uptake by the Novel ABC Transport System MusEFGK2I Causes Increased Expression of ptsG in Corynebacterium glutamicum

    PubMed Central

    Henrich, Alexander; Kuhlmann, Nora; Eck, Alexander W.; Krämer, Reinhard

    2013-01-01

    The Gram-positive Corynebacterium glutamicum efficiently metabolizes maltose by a pathway involving maltodextrin and glucose formation by 4-α-glucanotransferase, glucose phosphorylation by glucose kinases, and maltodextrin degradation via maltodextrin phosphorylase and α-phosphoglucomutase. However, maltose uptake in C. glutamicum has not been investigated. Interestingly, the presence of maltose in the medium causes increased expression of ptsG in C. glutamicum by an unknown mechanism, although the ptsG-encoded glucose-specific EII permease of the phosphotransferase system itself is not required for maltose utilization. We identified the maltose uptake system as an ABC transporter encoded by musK (cg2708; ATPase subunit), musE (cg2705; substrate binding protein), musF (cg2704; permease), and musG (cg2703; permease) by combination of data obtained from characterization of maltose uptake and reanalyses of transcriptome data. Deletion of the mus gene cluster in C. glutamicum Δmus abolished maltose uptake and utilization. Northern blotting and reverse transcription-PCR experiments revealed that musK and musE are transcribed monocistronically, whereas musF and musG are part of an operon together with cg2701 (musI), which encodes a membrane protein of unknown function with no homologies to characterized proteins. Characterization of growth and [14C]maltose uptake in the musI insertion strain C. glutamicum IMcg2701 showed that musI encodes a novel essential component of the maltose ABC transporter of C. glutamicum. Finally, ptsG expression during cultivation on different carbon sources was analyzed in the maltose uptake-deficient strain C. glutamicum Δmus. Indeed, maltose uptake by the novel ABC transport system MusEFGK2I is required for the positive effect of maltose on ptsG expression in C. glutamicum. PMID:23543710

  18. Expression of the agmatine deiminase pathway in Enterococcus faecalis is activated by the AguR regulator and repressed by CcpA and PTS(Man) systems.

    PubMed

    Suárez, Cristian; Espariz, Martín; Blancato, Víctor S; Magni, Christian

    2013-01-01

    Although the agmatine deiminase system (AgDI) has been investigated in Enterococcus faecalis, little information is available with respect to its gene regulation. In this study we demonstrate that the presence of exogenous agmatine induces the expression of agu genes in this bacterium. In contrast to the homologous and extensively characterized AgDI system of S. mutants, the aguBDAC operon in E. faecalis is not induced in response to low pH. In spite of this, agmatine catabolism in this bacterium contributes by neutralizing the external medium while enhancing bacterial growth. Our results indicate that carbon catabolic repression (CCR) operates on the AgDI system via a mechanism that involves interaction of CcpA and P-Ser-HPr with a cre site found in an unusual position considering the aguB promoter (55 nt upstream the +1 position). In addition, we found that components of the mannose phosphotransferase (PTS(Man)) system also contributed to CCR in E. faecalis since a complete relief of the PTS-sugars repressive effect was observed only in a PTS(Man) and CcpA double defective strain. Our gene context analysis revealed that aguR is present in oral and gastrointestinal microorganisms. Thus, regulation of the aguBDAC operon in E. faecalis seems to have evolved to obtain energy and resist low pH conditions in order to persist and colonize gastrointestinal niches. PMID:24155893

  19. A ptsP deficiency in PGPR Pseudomonas fluorescens SF39a affects bacteriocin production and bacterial fitness in the wheat rhizosphere.

    PubMed

    Godino, Agustina; Príncipe, Analía; Fischer, Sonia

    2016-04-01

    Pseudomonas fluorescens SF39a is a plant-growth-promoting bacterium isolated from wheat rhizosphere. In this report, we demonstrate that this native strain secretes bacteriocins that inhibit growth of phytopathogenic strains of the genera Pseudomonas and Xanthomonas. An S-type pyocin gene was detected in the genome of strain SF39a and named pys. A non-polar pys::Km mutant was constructed. The bacteriocin production was impaired in this mutant. To identify genes involved in bacteriocin regulation, random transposon mutagenesis was carried out. A miniTn5Km1 mutant, called P. fluorescens SF39a-451, showed strongly reduced bacteriocin production. This phenotype was caused by inactivation of the ptsP gene which encodes a phosphoenolpyruvate phosphotransferase (EI(Ntr)) of the nitrogen-related phosphotransferase system (PTS(Ntr)). In addition, this mutant showed a decrease in biofilm formation and protease production, and an increase in surface motility and pyoverdine production compared with the wild-type strain. Moreover, we investigated the ability of strain SF39a-451 to colonize the wheat rhizosphere under greenhouse conditions. Interestingly, the mutant was less competitive than the wild-type strain in the rhizosphere. To our knowledge, this study provides the first evidence of both the relevance of the ptsP gene in bacteriocin production and functional characterization of a pyocin S in P. fluorescens. PMID:26708985

  20. 224} studied by NMR

    SciTech Connect

    Furukawa, Y; Fang, X; Kögerler, P

    2014-05-14

    7Li nuclear magnetic resonance (NMR) studies have been performed to investigate magnetic properties and spin dynamics of Mn3+ (S = 2) spins in the giant polyoxometalate molecule {Mn40W224}. The 7Li-NMR line width is proportional to the external magnetic field H as expected in a paramagnetic state above 3 K. Below this temperature the line width shows a sudden increase and is almost independent of H, which indicates freezing of the local Mn3+ spins. The temperature dependence of T1 for both 1H and 7Li reveals slow spin dynamics at low temperatures, consistent with spin freezing. The slow spin dynamics is also evidenced by the observation of a peak of 1/T2 around 3 K, where the fluctuation frequency of spins is of the order of ~200 kHz. An explicit form of the temperature dependence of the fluctuation frequency of Mn3+ spins is derived from the nuclear relaxation data.

  1. The NMR phased array.

    PubMed

    Roemer, P B; Edelstein, W A; Hayes, C E; Souza, S P; Mueller, O M

    1990-11-01

    We describe methods for simultaneously acquiring and subsequently combining data from a multitude of closely positioned NMR receiving coils. The approach is conceptually similar to phased array radar and ultrasound and hence we call our techniques the "NMR phased array." The NMR phased array offers the signal-to-noise ratio (SNR) and resolution of a small surface coil over fields-of-view (FOV) normally associated with body imaging with no increase in imaging time. The NMR phased array can be applied to both imaging and spectroscopy for all pulse sequences. The problematic interactions among nearby surface coils is eliminated (a) by overlapping adjacent coils to give zero mutual inductance, hence zero interaction, and (b) by attaching low input impedance preamplifiers to all coils, thus eliminating interference among next nearest and more distant neighbors. We derive an algorithm for combining the data from the phased array elements to yield an image with optimum SNR. Other techniques which are easier to implement at the cost of lower SNR are explored. Phased array imaging is demonstrated with high resolution (512 x 512, 48-cm FOV, and 32-cm FOV) spin-echo images of the thoracic and lumbar spine. Data were acquired from four-element linear spine arrays, the first made of 12-cm square coils and the second made of 8-cm square coils. When compared with images from a single 15 x 30-cm rectangular coil and identical imaging parameters, the phased array yields a 2X and 3X higher SNR at the depth of the spine (approximately 7 cm). PMID:2266841

  2. NMR imaging of materials

    SciTech Connect

    Vinegar, H.J.; Rothwell, W.P.

    1988-03-01

    A method for obtaining at least one petrophysical property of a porous material containing therein at least one preselected fluid, is described, comprising: NMR imaging the material to generate signals dependent upon both M(0) and T/sub 1/ and M(0) and T/sub 2/, generating separate M(0), T/sub 1/ and T/sub 2/ images from the signals, and determining at least one petrophysical property from at least one of the images.

  3. NMR Studies of Peroxidases.

    NASA Astrophysics Data System (ADS)

    Veitch, Nigel Charles

    Available from UMI in association with The British Library. Requires signed TDF. Peroxidases are a haem-containing group of enzymes with a wide diversity of function within biological systems. While a common characteristic is the ability to catalyse the conversion of hydrogen peroxide to water, it is the accompanying processes of hormone synthesis and degradation which have generated such a high level of interest. However, information at the molecular level is limited to a single well-resolved crystal structure, that of yeast cytochrome c peroxidase. This thesis presents a strategy for the investigation of peroxidase structure and function based on proton nuclear magnetic resonance spectroscopy, a technique which has the ability to address aspects of both protein structure and protein dynamics in solution. The application of one- and two-dimensional NMR techniques has been developed in the context of plant peroxidases, notably the isoenzyme HRP-C derived from the horseradish root. Characterisation of the proton NMR spectra of HRP -C in resting and ligated states provided new information enabling the structure of the binding site for aromatic donor molecules, such as indole-3-propionic, ferulic and benzhydroxamic acids, to be resolved. In order to overcome difficulties encountered with a protein of the complexity of peroxidase, additional information was obtained from chemical shift parameters and the use of peroxidase variants produced by site-directed mutagenesis. A comparative study using NMR spectroscopy was undertaken for wild-type recombinant HRP-C expressed in Escherichia coli, and two protein variants with substitutions made to residues located on the distal side of the haem pocket, Phe41 to Val and Arg38 to Lys. NMR analyses of a plant peroxidase from barley grains and the fungal peroxidase from Coprinus cinereus were also successful using methods conceived with HRP-C. Examination of three specifically constructed recombinant protein variants of C. cinereus

  4. Bayesian reconstruction of projection reconstruction NMR (PR-NMR).

    PubMed

    Yoon, Ji Won

    2014-11-01

    Projection reconstruction nuclear magnetic resonance (PR-NMR) is a technique for generating multidimensional NMR spectra. A small number of projections from lower-dimensional NMR spectra are used to reconstruct the multidimensional NMR spectra. In our previous work, it was shown that multidimensional NMR spectra are efficiently reconstructed using peak-by-peak based reversible jump Markov chain Monte Carlo (RJMCMC) algorithm. We propose an extended and generalized RJMCMC algorithm replacing a simple linear model with a linear mixed model to reconstruct close NMR spectra into true spectra. This statistical method generates samples in a Bayesian scheme. Our proposed algorithm is tested on a set of six projections derived from the three-dimensional 700 MHz HNCO spectrum of a protein HasA. PMID:25218584

  5. Soils, Pores, and NMR

    NASA Astrophysics Data System (ADS)

    Pohlmeier, Andreas; Haber-Pohlmeier, Sabina; Haber, Agnes; Sucre, Oscar; Stingaciu, Laura; Stapf, Siegfried; Blümich, Bernhard

    2010-05-01

    Within Cluster A, Partial Project A1, the pore space exploration by means of Nuclear Magnetic Resonance (NMR) plays a central role. NMR is especially convenient since it probes directly the state and dynamics of the substance of interest: water. First, NMR is applied as relaxometry, where the degree of saturation but also the pore geometry controls the NMR signature of natural porous systems. Examples are presented where soil samples from the Selhausen, Merzenhausen (silt loams), and Kaldenkirchen (sandy loam) test sites are investigated by means of Fast Field Cycling Relaxometry at different degrees of saturation. From the change of the relaxation time distributions with decreasing water content and by comparison with conventional water retention curves we conclude that the fraction of immobile water is characterized by T1 < 5 ms. Moreover, the dependence of the relaxation rate on magnetic field strength allows the identification of 2D diffusion at the interfaces as the mechanism which governs the relaxation process (Pohlmeier et al. 2009). T2 relaxation curves are frequently measured for the rapid characterization of soils by means of the CPMG echo train. Basically, they contain the same information about the pore systems like T1 curves, since mostly the overall relaxation is dominated by surface relaxivity and the surface/volume ratio of the pores. However, one must be aware that T2 relaxation is additionally affected by diffusion in internal gradients, and this can be overcome by using sufficiently short echo times and low magnetic fields (Stingaciu et al. 2009). Second, the logic continuation of conventional relaxation measurements is the 2-dimensional experiment, where prior to the final detection of the CPMG echo train an encoding period is applied. This can be T1-encoding by an inversion pulse, or T2 encoding by a sequence of 90 and 180° pulses. During the following evolution time the separately encoded signals can mix and this reveals information about

  6. Summary of Miniature NMR Development

    SciTech Connect

    Friedman, Gennady; Feinerman, Alan

    2000-12-31

    The effort in this project has been in 3 distinct directions: (1) First, they focused on development of miniature microfabricated micro-coil NMR detectors with maximum Signal-to-Noise (SNR) ratio. (2) Secondly, they focused on design of miniature micro-coil NMR detectors that have minimal effect on the NMR spectrum distortions. (3) Lastly they focused on the development of a permanent magnet capable of generating fields on the order of 1 Tesla with better than 10 ppm uniformity.

  7. Temperature-Dependent Expression of phzM and Its Regulatory Genes lasI and ptsP in Rhizosphere Isolate Pseudomonas sp. Strain M18▿

    PubMed Central

    Huang, Jiaofang; Xu, Yuquan; Zhang, Hongyan; Li, Yaqian; Huang, Xianqing; Ren, Bin; Zhang, Xuehong

    2009-01-01

    Pseudomonas sp. strain M18, an effective biological control agent isolated from the melon rhizosphere, has a genetic background similar to that of the opportunistic human pathogen Pseudomonas aeruginosa PAO1. However, the predominant phenazine produced by strain M18 is phenazine-1-carboxylic acid (PCA) rather than pyocyanin (PYO); the quantitative ratio of PCA to PYO is 105 to 1 at 28°C in strain M18, while the ratio is 1 to 2 at 37°C in strain PAO1. We first provided evidence that the differential production of the two phenazines in strains M18 and PAO1 is related to the temperature-dependent and strain-specific expression patterns of phzM, a gene involved in the conversion of PCA to PYO. Transcriptional levels of phzM were measured by quantitative real-time PCR, and the activities of both transcriptional and translational phzM′-′lacZ fusions were determined in strains M18 and PAO1, respectively. Using lasI::Gm and ptsP::Gm inactivation M18 mutants, we further show that expression of the phzM gene is positively regulated by the quorum-sensing protein LasI and negatively regulated by the phosphoenolpyruvate phosphotransferase protein PtsP. Surprisingly, the lasI and ptsP regulatory genes were also expressed in a temperature-dependent and strain-specific manner. The differential production of the phenazines PCA and PYO by strains M18 and PAO1 may be a consequence of selective pressure imposed on P. aeruginosa PAO1 and its relative M18 in the two different niches over a long evolutionary process. PMID:19717631

  8. THz Dynamic Nuclear Polarization NMR

    PubMed Central

    Nanni, Emilio A.; Barnes, Alexander B.; Griffin, Robert G.; Temkin, Richard J.

    2013-01-01

    Dynamic nuclear polarization (DNP) increases the sensitivity of nuclear magnetic resonance (NMR) spectroscopy by using high frequency microwaves to transfer the polarization of the electrons to the nuclear spins. The enhancement in NMR sensitivity can amount to a factor of well above 100, enabling faster data acquisition and greatly improved NMR measurements. With the increasing magnetic fields (up to 23 T) used in NMR research, the required frequency for DNP falls into the THz band (140–600 GHz). Gyrotrons have been developed to meet the demanding specifications for DNP NMR, including power levels of tens of watts; frequency stability of a few megahertz; and power stability of 1% over runs that last for several days to weeks. Continuous gyrotron frequency tuning of over 1 GHz has also been demonstrated. The complete DNP NMR system must include a low loss transmission line; an optimized antenna; and a holder for efficient coupling of the THz radiation to the sample. This paper describes the DNP NMR process and illustrates the THz systems needed for this demanding spectroscopic application. THz DNP NMR is a rapidly developing, exciting area of THz science and technology. PMID:24639915

  9. THz Dynamic Nuclear Polarization NMR.

    PubMed

    Nanni, Emilio A; Barnes, Alexander B; Griffin, Robert G; Temkin, Richard J

    2011-08-29

    Dynamic nuclear polarization (DNP) increases the sensitivity of nuclear magnetic resonance (NMR) spectroscopy by using high frequency microwaves to transfer the polarization of the electrons to the nuclear spins. The enhancement in NMR sensitivity can amount to a factor of well above 100, enabling faster data acquisition and greatly improved NMR measurements. With the increasing magnetic fields (up to 23 T) used in NMR research, the required frequency for DNP falls into the THz band (140-600 GHz). Gyrotrons have been developed to meet the demanding specifications for DNP NMR, including power levels of tens of watts; frequency stability of a few megahertz; and power stability of 1% over runs that last for several days to weeks. Continuous gyrotron frequency tuning of over 1 GHz has also been demonstrated. The complete DNP NMR system must include a low loss transmission line; an optimized antenna; and a holder for efficient coupling of the THz radiation to the sample. This paper describes the DNP NMR process and illustrates the THz systems needed for this demanding spectroscopic application. THz DNP NMR is a rapidly developing, exciting area of THz science and technology. PMID:24639915

  10. Two-dimensional NMR spectroscopy

    SciTech Connect

    Croasmun, W.R.; Carlson, R.M.K.

    1987-01-01

    Written for chemists and biochemists who are not NMR spectroscopists, but who wish to use the new techniques of two-dimensional NMR spectroscopy, this book brings together for the first time much of the practical and experimental data needed. It also serves as information source for industrial, academic, and graduate student researchers who already use NMR spectroscopy, but not yet in two dimensions. The authors describe the use of 2-D NMR in a wide variety of chemical and biochemical fields, among them peptides, steroids, oligo- and poly-saccharides, nucleic acids, natural products (including terpenoids, alkaloids, and coal-derived heterocyclics), and organic synthetic intermediates. They consider throughout the book both the advantages and limitations of using 2-D NMR.

  11. PTS regulation domain-containing transcriptional activator CelR and sigma factor σ(54) control cellobiose utilization in Clostridium acetobutylicum.

    PubMed

    Nie, Xiaoqun; Yang, Bin; Zhang, Lei; Gu, Yang; Yang, Sheng; Jiang, Weihong; Yang, Chen

    2016-04-01

    The phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) regulation domain (PRD)-containing enhancer binding proteins (EBPs) are an important class of σ(54) -interacting transcriptional activators. Although PRD-containing EBPs are present in many Firmicutes, most of their regulatory functions remain unclear. In this study, the transcriptional regulons of about 50 PRD-containing EBPs in diverse Firmicutes species are reconstructed by using a comparative genomic approach, which contain the genes associated with utilization of β-glucosides, fructose/levan, mannose/glucose, pentitols, and glucosamine/fructosamine. We then present experimental evidence that the cel operon involved in cellobiose utilization is directly regulated by CelR and σ(54) (SigL) in Clostridium acetobutylicum. The predicted three CelR-binding sites and σ(54) promoter elements upstream of the cel operon are verified by in vitro binding assays. We show that CelR has an ATPase activity, which is strongly stimulated by the presence of DNA containing the CelR-binding sites. Moreover, mutations in any one of the three CelR-binding sites significantly decreased the cel promoter activity probably due to the need for all three DNA sites for maximal ATPase activity of CelR. It is suggested that CelR is regulated by PTS-mediated phosphorylation at His-551 and His-829, which exerts a positive effect and an inhibitory effect, respectively, on the CelR activity. PMID:26691835

  12. Compact orthogonal NMR field sensor

    DOEpatents

    Gerald, II, Rex E.; Rathke, Jerome W.

    2009-02-03

    A Compact Orthogonal Field Sensor for emitting two orthogonal electro-magnetic fields in a common space. More particularly, a replacement inductor for existing NMR (Nuclear Magnetic Resonance) sensors to allow for NMR imaging. The Compact Orthogonal Field Sensor has a conductive coil and a central conductor electrically connected in series. The central conductor is at least partially surrounded by the coil. The coil and central conductor are electrically or electro-magnetically connected to a device having a means for producing or inducing a current through the coil and central conductor. The Compact Orthogonal Field Sensor can be used in NMR imaging applications to determine the position and the associated NMR spectrum of a sample within the electro-magnetic field of the central conductor.

  13. Integrative NMR for biomolecular research.

    PubMed

    Lee, Woonghee; Cornilescu, Gabriel; Dashti, Hesam; Eghbalnia, Hamid R; Tonelli, Marco; Westler, William M; Butcher, Samuel E; Henzler-Wildman, Katherine A; Markley, John L

    2016-04-01

    NMR spectroscopy is a powerful technique for determining structural and functional features of biomolecules in physiological solution as well as for observing their intermolecular interactions in real-time. However, complex steps associated with its practice have made the approach daunting for non-specialists. We introduce an NMR platform that makes biomolecular NMR spectroscopy much more accessible by integrating tools, databases, web services, and video tutorials that can be launched by simple installation of NMRFAM software packages or using a cross-platform virtual machine that can be run on any standard laptop or desktop computer. The software package can be downloaded freely from the NMRFAM software download page ( http://pine.nmrfam.wisc.edu/download_packages.html ), and detailed instructions are available from the Integrative NMR Video Tutorial page ( http://pine.nmrfam.wisc.edu/integrative.html ). PMID:27023095

  14. Polarization transfer NMR imaging

    DOEpatents

    Sillerud, Laurel O.; van Hulsteyn, David B.

    1990-01-01

    A nuclear magnetic resonance (NMR) image is obtained with spatial information modulated by chemical information. The modulation is obtained through polarization transfer from a first element representing the desired chemical, or functional, information, which is covalently bonded and spin-spin coupled with a second element effective to provide the imaging data. First and second rf pulses are provided at first and second frequencies for exciting the imaging and functional elements, with imaging gradients applied therebetween to spatially separate the nuclei response for imaging. The second rf pulse is applied at a time after the first pulse which is the inverse of the spin coupling constant to select the transfer element nuclei which are spin coupled to the functional element nuclei for imaging. In a particular application, compounds such as glucose, lactate, or lactose, can be labeled with .sup.13 C and metabolic processes involving the compounds can be imaged with the sensitivity of .sup.1 H and the selectivity of .sup.13 C.

  15. Optical pumping and xenon NMR

    SciTech Connect

    Raftery, M.D.

    1991-11-01

    Nuclear Magnetic Resonance (NMR) spectroscopy of xenon has become an important tool for investigating a wide variety of materials, especially those with high surface area. The sensitivity of its chemical shift to environment, and its chemical inertness and adsorption properties make xenon a particularly useful NMR probe. This work discusses the application of optical pumping to enhance the sensitivity of xenon NMR experiments, thereby allowing them to be used in the study of systems with lower surface area. A novel method of optically-pumping [sup 129]Xe in low magnetic field below an NMR spectrometer and subsequent transfer of the gas to high magnetic field is described. NMR studies of the highly polarized gas adsorbed onto powdered samples with low to moderate surface areas are now possible. For instance, NMR studies of optically-pumped xenon adsorbed onto polyacrylic acid show that xenon has a large interaction with the surface. By modeling the low temperature data in terms of a sticking probability and the gas phase xenon-xenon interaction, the diffusion coefficient for xenon at the surface of the polymer is determined. The sensitivity enhancement afforded by optical pumping also allows the NMR observation of xenon thin films frozen onto the inner surfaces of different sample cells. The geometry of the thin films results in interesting line shapes that are due to the bulk magnetic susceptibility of xenon. Experiments are also described that combine optical pumping with optical detection for high sensitivity in low magnetic field to observe the quadrupoler evolution of 131 Xe spins at the surface of the pumping cells. In cells with macroscopic asymmetry, a residual quadrupolar interaction causes a splitting in the [sup 131]Xe NMR frequencies in bare Pyrex glass cells and cells with added hydrogen.

  16. Optical pumping and xenon NMR

    SciTech Connect

    Raftery, M.D.

    1991-11-01

    Nuclear Magnetic Resonance (NMR) spectroscopy of xenon has become an important tool for investigating a wide variety of materials, especially those with high surface area. The sensitivity of its chemical shift to environment, and its chemical inertness and adsorption properties make xenon a particularly useful NMR probe. This work discusses the application of optical pumping to enhance the sensitivity of xenon NMR experiments, thereby allowing them to be used in the study of systems with lower surface area. A novel method of optically-pumping {sup 129}Xe in low magnetic field below an NMR spectrometer and subsequent transfer of the gas to high magnetic field is described. NMR studies of the highly polarized gas adsorbed onto powdered samples with low to moderate surface areas are now possible. For instance, NMR studies of optically-pumped xenon adsorbed onto polyacrylic acid show that xenon has a large interaction with the surface. By modeling the low temperature data in terms of a sticking probability and the gas phase xenon-xenon interaction, the diffusion coefficient for xenon at the surface of the polymer is determined. The sensitivity enhancement afforded by optical pumping also allows the NMR observation of xenon thin films frozen onto the inner surfaces of different sample cells. The geometry of the thin films results in interesting line shapes that are due to the bulk magnetic susceptibility of xenon. Experiments are also described that combine optical pumping with optical detection for high sensitivity in low magnetic field to observe the quadrupoler evolution of 131 Xe spins at the surface of the pumping cells. In cells with macroscopic asymmetry, a residual quadrupolar interaction causes a splitting in the {sup 131}Xe NMR frequencies in bare Pyrex glass cells and cells with added hydrogen.

  17. Multispectral Analysis of NMR Imagery

    NASA Technical Reports Server (NTRS)

    Butterfield, R. L.; Vannier, M. W. And Associates; Jordan, D.

    1985-01-01

    Conference paper discusses initial efforts to adapt multispectral satellite-image analysis to nuclear magnetic resonance (NMR) scans of human body. Flexibility of these techniques makes it possible to present NMR data in variety of formats, including pseudocolor composite images of pathological internal features. Techniques do not have to be greatly modified from form in which used to produce satellite maps of such Earth features as water, rock, or foliage.

  18. NMR characterization of thin films

    DOEpatents

    Gerald II, Rex E.; Klingler, Robert J.; Rathke, Jerome W.; Diaz, Rocio; Vukovic, Lela

    2010-06-15

    A method, apparatus, and system for characterizing thin film materials. The method, apparatus, and system includes a container for receiving a starting material, applying a gravitational force, a magnetic force, and an electric force or combinations thereof to at least the starting material, forming a thin film material, sensing an NMR signal from the thin film material and analyzing the NMR signal to characterize the thin film of material.

  19. NMR characterization of thin films

    DOEpatents

    Gerald, II, Rex E.; Klingler, Robert J.; Rathke, Jerome W.; Diaz, Rocio; Vukovic, Lela

    2008-11-25

    A method, apparatus, and system for characterizing thin film materials. The method, apparatus, and system includes a container for receiving a starting material, applying a gravitational force, a magnetic force, and an electric force or combinations thereof to at least the starting material, forming a thin film material, sensing an NMR signal from the thin film material and analyzing the NMR signal to characterize the thin film of material.

  20. Construction of Listeria monocytogenes mutants with in-frame deletions in the phosphotransferase transport system (PTS) and analysis of their growth under stress conditions.

    PubMed

    Liu, Yanhong; Ceruso, Marina; Jiang, Yuji; Datta, Atin R; Carter, Laurenda; Strain, Errol; Pepe, Tiziana; Anastasi, Aniello; Fratamico, Pina

    2013-09-01

    Listeria monocytogenes is a foodborne pathogen that is difficult to eliminate due to its ability to survive under different stress conditions such as low pH and high salt. To better control this pathogen in food, it is important to understand its survival mechanisms under these stress conditions. LMOf2365_0442, 0443, and 0444 encode for phosphotransferase transport system (PTS) permease (fructose-specific IIABC components) that is responsible for sugar transport. LMOf2365_0445 encodes for glycosyl hydrolase. These genes were induced by high pressure and inhibited under salt treatments; therefore, we hypothesized that genes encoding these PTS proteins may be involved in general stress responses. To study the function of these genes, deletion mutants of the PTS genes (LMOf2365_0442, LMOf2365_0443, and LMOf2365_0444) and the downstream gene LMOf2365_0445 were created in L. monocytogenes strain F2365. These deletion mutants were tested under different stress conditions. The growth of ∆LMOf2365_0445 was increased under nisin (125 μg/mL) treatments compared to the wild-type (P < 0.01). The growth of ∆LMOf2365_0442 in salt (brain-heart infusion medium with 5% NaCl) was significantly increased (P < 0.01), and ∆LMOf2365_0442 showed increased growth under acidic conditions (pH 5.0) compared to the wild-type (P < 0.01). The results from phenotypic arrays demonstrated that some of these mutants showed slightly slower growth under different carbon sources and basic conditions. The results indicate that deletion mutants ∆LMOf2365_0442 and ∆LMOf2365_0445 were more resistant to multiple stress conditions compared to the wild-type, suggesting that they may contribute to the general stress response in L. monocytogenes. An understanding of the growth of these mutants under multiple stress conditions may assist in the development of intervention strategies to control L. monocytogenes in food. PMID:23909479

  1. Automated protein NMR resonance assignments.

    PubMed

    Wan, Xiang; Xu, Dong; Slupsky, Carolyn M; Lin, Guohui

    2003-01-01

    NMR resonance peak assignment is one of the key steps in solving an NMR protein structure. The assignment process links resonance peaks to individual residues of the target protein sequence, providing the prerequisite for establishing intra- and inter-residue spatial relationships between atoms. The assignment process is tedious and time-consuming, which could take many weeks. Though there exist a number of computer programs to assist the assignment process, many NMR labs are still doing the assignments manually to ensure quality. This paper presents (1) a new scoring system for mapping spin systems to residues, (2) an automated adjacency information extraction procedure from NMR spectra, and (3) a very fast assignment algorithm based on our previous proposed greedy filtering method and a maximum matching algorithm to automate the assignment process. The computational tests on 70 instances of (pseudo) experimental NMR data of 14 proteins demonstrate that the new score scheme has much better discerning power with the aid of adjacency information between spin systems simulated across various NMR spectra. Typically, with automated extraction of adjacency information, our method achieves nearly complete assignments for most of the proteins. The experiment shows very promising perspective that the fast automated assignment algorithm together with the new score scheme and automated adjacency extraction may be ready for practical use. PMID:16452794

  2. NMR Relaxation and Petrophysical Properties

    NASA Astrophysics Data System (ADS)

    Fleury, Marc

    2011-03-01

    NMR relaxation is routinely used in the field of geosciences to give basic petrophysical properties such as porosity, pore size distribution, saturation etc. In this tutorial, we focus on the pore size distribution deduced from NMR. We recall the basic principle used in the interpretation of the NMR signal and compare the results with other standard petrophysical techniques such as mercury pore size distribution, BET specific surface measurements, thin section visualizations. The NMR pore size distribution is a unique information available on water saturated porous media and can give similar results as MICP in certain situations. The scaling of NMR relaxation time distribution (s) into pore sizes (μm) requires the knowledge of the surface relaxivity (μm/s) and we recommend using specific surface measurements as an independent determination of solid surface areas. With usual surface relaxivities, the NMR technique can explore length-scales starting from nano-meters and ending around 100 μm. Finally, we will introduce briefly recent techniques sensitive to the pore to pore diffusional exchange, providing new information on the connectivity of the pore network, but showing another possibility of discrepancy in the determination of pore size distribution with standard techniques.

  3. A sigma(54)-dependent PTS permease of the mannose family is responsible for sensitivity of Listeria monocytogenes to mesentericin Y105.

    PubMed

    Dalet, K; Cenatiempo, Y; Cossart, P; Héchard, Y

    2001-12-01

    Sensitivity of Listeria monocytogenes to the bacteriocin mesentericin Y105 was previously shown to be dependent on the sigma(54) subunit of the RNA polymerase. This points towards expression of particular sigma(54)-dependent genes. The present study describes first, ManR, a new sigma(54)-associated activator, and second, Ell(t)(Man), a new sigma(54)-dependent PTS permease of the mannose family, both involved in sensitivity to mesentericin Y105, since interruption of their corresponding genes led to resistance of L. monocytogenes EGDe. Ell(t)(Man) is likely composed of three subunits encoded by the mpt operon (mptA, mptC and mptD genes). Interruption of either the proximal (mptA) or distal (mptD) gene led to resistance, supporting results obtained in Enterococcus faecalis. Accordingly, such PTS permeases of the mannose family should be involved in sensitivity of different target strains to mesentericin Y105. In L. monocytogenes, expression of the mpt operon is shown to be controlled by sigma(54) and ManR and to be induced by both glucose and mannose. The latter result indicates that these sugars are transported by the Ell(t)(Man) permease. Moreover, these sugars correlatively induce sensitivity of L. monocytogenes to mesentericin Y105, strongly favouring the primary role of Ell(t)(Man). MptD, a membrane subunit of Ell(t)(Man), presents an additional domain compared to most IID(Man) subunits described in data banks. An in-frame deletion of this domain in mptD led to resistance of L. monocytogenes, showing its connection with sensitivity and suggesting that it could be directly involved in the recognition of the target cell by mesentericin Y105. Taken together, the results of this work demonstrate that Ell(t)(Man) is prominent in sensitivity to mesentericin Y105 and could be a receptor for subclass IIa bacteriocins. PMID:11739758

  4. Medical applications of NMR imaging and NMR spectroscopy with stable isotopes. Summary

    SciTech Connect

    Matwiyoff, N.A.

    1983-01-01

    The current status of NMR imaging and NMR spectroscopy are summarized. For the most part examples from the March 1983 Puerto Rico symposium are used to illustrate the utility of NMR in medicine. 18 refs., 5 figs.

  5. jsNMR: an embedded platform-independent NMR spectrum viewer.

    PubMed

    Vosegaard, Thomas

    2015-04-01

    jsNMR is a lightweight NMR spectrum viewer written in JavaScript/HyperText Markup Language (HTML), which provides a cross-platform spectrum visualizer that runs on all computer architectures including mobile devices. Experimental (and simulated) datasets are easily opened in jsNMR by (i) drag and drop on a jsNMR browser window, (ii) by preparing a jsNMR file from the jsNMR web site, or (iii) by mailing the raw data to the jsNMR web portal. jsNMR embeds the original data in the HTML file, so a jsNMR file is a self-transforming dataset that may be exported to various formats, e.g. comma-separated values. The main applications of jsNMR are to provide easy access to NMR data without the need for dedicated software installed and to provide the possibility to visualize NMR spectra on web sites. PMID:25641013

  6. NMR Imaging: Instrumentation and Techniques

    NASA Astrophysics Data System (ADS)

    Tingle, Jeremy Mark

    Available from UMI in association with The British Library. This thesis presents three original contributions to the field of Nuclear Magnetic Resonance (NMR): the experimental framework and analysis for the measurement of a new imaging parameter to describe perfusion; the measurement and analysis of magnetic field inhomogeneity and a practical correction system for their reduction; a novel system for the synchronous control of NMR experiments based on the microprogrammed concept. The thesis begins with an introduction to the theory of NMR. The application of NMR to imaging is also introduced with emphasis on the techniques which developed into those in common use today. Inaccurate determination of the traditional NMR parameters (T_1 and T_2 and the molecular diffusion coefficient) can be caused by non-diffusive fluid movement within the sample. The experimental basis for determining a new imaging parameter --the Perfusion coefficient--is presented. This provides a measure of forced isotropic fluid motion through an organ or tissue. The instrumentation required for conducting NMR experiments is described in order to introduce the contribution made in this area during this research: A sequence controller. The controller is based on the concept of microprogramming and enables completely synchronous output of 128 bits of data. The software for the generation and storage of control data and the regulation of the data to provide experimental control is microcomputer based. It affords precise and accurate regulation of the magnetic field gradients, the rf synthesizer and the spectrometer for spectroscopic and imaging applications. Fundamental to the science of NMR is the presence of a magnetic field. A detailed study of the analysis of magnetic field inhomogeneity in terms of spherical harmonics is presented. The field of a whole body imaging system with poor inhomogeneity was measured and analyzed to determine and describe the components of the inhomogeneity. Finally a

  7. NMR planar microcoil for microanalysis

    NASA Astrophysics Data System (ADS)

    Sorli, B.; Chateaux, J. F.; Quiquerez, L.; Bouchet-Fakri, L.; Briguet, A.; Morin, P.

    2006-11-01

    This article deals with the analysis of small sample volume by using a planar microcoil and a micromachined cavity. This microcoil is used as a nuclear magnetic resonance (NMR) radio frequency detection coil in order to perform in vitro NMR analysis of the sample introduced into the microcavity. It is a real challenging task to develop microsystem for NMR spectrum extraction for smaller and smaller sample volume. Moreover, it is advantageous that these microsystems could be integrated in a Micro Total Analysing System (μ -TAS) as an analysing tool. In this paper, NMR theory, description, fabrication process and electrical characterization of planar microcoils receiver are described. Results obtained on NMR microspectroscopy experiments have been performed on water and ethanol, using a 1 mm diameter planar coil. This microcoil is tuned and matched at 85.13 MHz which is the Larmor frequency of proton in a 2 T magnetic field. This paper has been presented at “3e colloque interdisciplinaire en instrumentation (C2I 2004)”, École Normale Supérieure de Cachan, 29 30 janvier 2004.

  8. Improving NMR Structures of RNA.

    PubMed

    Bermejo, Guillermo A; Clore, G Marius; Schwieters, Charles D

    2016-05-01

    Here, we show that modern solution nuclear magnetic resonance (NMR) structures of RNA exhibit more steric clashes and conformational ambiguities than their crystallographic X-ray counterparts. To tackle these issues, we developed RNA-ff1, a new force field for structure calculation with Xplor-NIH. Using seven published NMR datasets, RNA-ff1 improves covalent geometry and MolProbity validation criteria for clashes and backbone conformation in most cases, relative to both the previous Xplor-NIH force field and the original structures associated with the experimental data. In addition, with smaller base-pair step rises in helical stems, RNA-ff1 structures enjoy more favorable base stacking. Finally, structural accuracy improves in the majority of cases, as supported by complete residual dipolar coupling cross-validation. Thus, the reported advances show great promise in bridging the quality gap that separates NMR and X-ray structures of RNA. PMID:27066747

  9. A SENSITIVE NMR THERMOMETER FOR MULTINUCLEI FT NMR

    EPA Science Inventory

    A pernicious problem in multinuclei FT NMR is accurate measurement of sample temperature. This arises from several factors including widespread use of high-power decoupling, large sample tubes (with potentially large temperature gradients across the sample volume), and lack of su...

  10. Protein-Inhibitor Interaction Studies Using NMR

    PubMed Central

    Ishima, Rieko

    2015-01-01

    Solution-state NMR has been widely applied to determine the three-dimensional structure, dynamics, and molecular interactions of proteins. The designs of experiments used in protein NMR differ from those used for small-molecule NMR, primarily because the information available prior to an experiment, such as molecular mass and knowledge of the primary structure, is unique for proteins compared to small molecules. In this review article, protein NMR for structural biology is introduced with comparisons to small-molecule NMR, such as descriptions of labeling strategies and the effects of molecular dynamics on relaxation. Next, applications for protein NMR are reviewed, especially practical aspects for protein-observed ligand-protein interaction studies. Overall, the following topics are described: (1) characteristics of protein NMR, (2) methods to detect protein-ligand interactions by NMR, and (3) practical aspects of carrying out protein-observed inhibitor-protein interaction studies. PMID:26361636

  11. "Solvent Effects" in 1H NMR Spectroscopy.

    ERIC Educational Resources Information Center

    Cavaleiro, Jose A. S.

    1987-01-01

    Describes a simple undergraduate experiment in chemistry dealing with the "solvent effects" in nuclear magnetic resonance (NMR) spectroscopy. Stresses the importance of having students learn NMR spectroscopy as a tool in analytical chemistry. (TW)

  12. Push-through Direction Injectin NMR Automation

    EPA Science Inventory

    Nuclear magnetic resonance (NMR) and mass spectrometry (MS) are the two major spectroscopic techniques successfully used in metabolomics studies. The non-invasive, quantitative and reproducible characteristics make NMR spectroscopy an excellent technique for detection of endogeno...

  13. Deuterium Exchange Kinetics by NMR.

    ERIC Educational Resources Information Center

    Roper, G. C.

    1985-01-01

    Describes a physical chemistry experiment which allows such concepts as kinetics, catalysis, isotope shifts, coupling constants, and the use of nuclear magnetic resonance (NMR) for quantitative work to be covered in the same exercise. Background information, experimental procedures used, and typical results obtained are included. (JN)

  14. Petrophysical applications of NMR imaging

    SciTech Connect

    Rothwell, W.P.; Vinegar, H.J.

    1985-12-01

    A system for obtaining high-resolution NMR images of oil field cores is described. Separate proton density and T/sub 2/ relaxation images are obtained to distinguish spatial variations of fluid-filled porosity and the physical nature of the pores. Results are presented for typical sandstones.

  15. QUANTITATIVE 15N NMR SPECTROSCOPY

    EPA Science Inventory

    Line intensities in 15N NMR spectra are strongly influenced by spin-lattice and spin-spin relaxation times, relaxation mechanisms and experimental conditions. Special care has to be taken in using 15N spectra for quantitative purposes. Quantitative aspects are discussed for the 1...

  16. Optimized multiple quantum MAS lineshape simulations in solid state NMR

    NASA Astrophysics Data System (ADS)

    Brouwer, William J.; Davis, Michael C.; Mueller, Karl T.

    2009-10-01

    /Linux Operating system: UNIX/Linux Has the code been vectorised or parallelized?: Yes RAM: Example: (1597 powder angles) × (200 Samples) × (81 F2 frequency pts) × (31 F1 frequency points) = 3.5M, SMP AMD opteron Classification: 2.3 External routines: OCTAVE ( http://www.gnu.org/software/octave/), GNU Scientific Library ( http://www.gnu.org/software/gsl/), OPENMP ( http://openmp.org/wp/) Nature of problem: The optimal simulation and modeling of multiple quantum magic angle spinning NMR spectra, for general systems, especially those with mild to significant disorder. The approach outlined and implemented in C and OCTAVE also produces model parameter error estimates. Solution method: A model for each distinct chemical site is first proposed, for the individual contribution of crystallite orientations to the spectrum. This model is averaged over all powder angles [1], as well as the (stochastic) parameters; isotropic chemical shift and quadrupole coupling constant. The latter is accomplished via sampling from a bi-variate Gaussian distribution, using the Box-Muller algorithm to transform Sobol (quasi) random numbers [2]. A simulated annealing optimization is performed, and finally the non-linear jackknife [3] is applied in developing model parameter error estimates. Additional comments: The distribution contains a script, mqmasOpt.m, which runs in the OCTAVE language workspace. Running time: Example: (1597 powder angles) × (200 Samples) × (81 F2 frequency pts) × (31 F1 frequency points) = 58.35 seconds, SMP AMD opteron. References:S.K. Zaremba, Annali di Matematica Pura ed Applicata 73 (1966) 293. H. Niederreiter, Random Number Generation and Quasi-Monte Carlo Methods, SIAM, 1992. T. Fox, D. Hinkley, K. Larntz, Technometrics 22 (1980) 29.

  17. Two dimensional NMR and NMR relaxation studies of coal structure

    SciTech Connect

    Zilm, K.W.

    1992-05-27

    This report covers the progress made on the title project for the project period. Four major areas of inquiry are being pursued. Advanced solid state NMR methods are being developed to assay the distribution of the various important functional groups that determine the reactivity of coals. Special attention is being paid to methods that are compatible with the very high magic angle sample spinning rates needed for operation at the high magnetic field strengths available today. Polarization inversion methods utilizing the difference in heat capacities of small groups of spins are particularly promising. Methods combining proton-proton spin diffusion with {sup 13}C CPMAS readout are being developed to determine the connectivity of functional groups in coals in a high sensitivity relay type of experiment. Additional work is aimed a delineating the role of methyl group rotation in the proton NMR relaxation behavior of coals.

  18. Carbon Catabolite Repression and the Related Genes of ccpA, ptsH and hprK in Thermoanaerobacterium aotearoense

    PubMed Central

    Zhu, Muzi; Lu, Yanping; Wang, Jufang; Li, Shuang; Wang, Xiaoning

    2015-01-01

    The strictly anaerobic, Gram-positive bacterium, Thermoanaerobacterium aotearoense SCUT27, is capable of producing ethanol, hydrogen and lactic acid by directly fermenting glucan, xylan and various lignocellulosically derived sugars. By using non-metabolizable and metabolizable sugars as substrates, we found that cellobiose, galactose, arabinose and starch utilization was strongly inhibited by the existence of 2-deoxyglucose (2-DG). However, the xylose and mannose consumptions were not markedly affected by 2-DG at the concentration of one-tenth of the metabolizable sugar. Accordingly, T. aotearoense SCUT27 could consume xylose and mannose in the presence of glucose. The carbon catabolite repression (CCR) related genes, ccpA, ptsH and hprK were confirmed to exist in T. aotearoense SCUT27 through gene cloning and protein characterization. The highly purified Histidine-containing Protein (HPr) could be specifically phosphorylated at Serine 46 by HPr kinase/phosphatase (HPrK/P) with no need to add fructose-1,6-bisphosphate (FBP) or glucose-6-phosphate (Glc-6-P) in the reaction mixture. The specific protein-interaction of catabolite control protein A (CcpA) and phosphorylated HPr was proved via affinity chromatography in the absence of formaldehyde. The equilibrium binding constant (KD) of CcpA and HPrSerP was determined as 2.22 ± 0.36 nM by surface plasmon resonance (SPR) analysis, indicating the high affinity between these two proteins. PMID:26540271

  19. Solution NMR of large molecules and assemblies†

    PubMed Central

    Foster, Mark P.; McElroy, Craig A.; Amero, Carlos D.

    2008-01-01

    Solution NMR spectroscopy represents a powerful tool for examining the structure and function of biological macromolecules. The advent of multidimensional (2D–4D) NMR, together with the widespread use of uniform isotopic labeling of proteins and RNA with the NMR-active isotopes, 15N and 13C, opened the door to detailed analyses of macromolecular structure, dynamics and interactions of smaller macromolecules (< ~25 kDa). Over the past 10 years, advances in NMR and isotope labeling methods have expanded the range of NMR-tractable targets by at least an order of magnitude. Here we briefly describe the methodological advances that allow NMR spectroscopy of large macromolecules and their complexes, and provide a perspective on the wide range of applications of NMR to biochemical problems. PMID:17209543

  20. Two-dimensional NMR spectrometry

    SciTech Connect

    Farrar, T.C.

    1987-06-01

    This article is the second in a two-part series. In part one (ANALYTICAL CHEMISTRY, May 15) the authors discussed one-dimensional nuclear magnetic resonance (NMR) spectra and some relatively advanced nuclear spin gymnastics experiments that provide a capability for selective sensitivity enhancements. In this article and overview and some applications of two-dimensional NMR experiments are presented. These powerful experiments are important complements to the one-dimensional experiments. As in the more sophisticated one-dimensional experiments, the two-dimensional experiments involve three distinct time periods: a preparation period, t/sub 0/; an evolution period, t/sub 1/; and a detection period, t/sub 2/.

  1. NMR investigation of Ag nanoparticles

    NASA Astrophysics Data System (ADS)

    Son, Kwanghyo; Jang, Zeehoon

    2013-01-01

    109Ag nuclear magnetic resonance (NMR) and relaxation measurements have been performed on two powder samples of Ag nanoparticles with average sizes of 20 nm and 80 nm. The measurements have been done in an external field of 9.4 T and in the temperature range 10 K < T < 280 K. The 109Ag NMR spectra for both samples have close to Lorentzian shapes and turn out to be mixtures of homogeneous and inhomogeneous lines. The linewidth Δ ν at room temperature is 1.3 kHz for both samples and gradually increases with decreasing temperature. Both the Knight shift ( K) and the nuclear spin-lattice relaxation rate (1/ T 1) are observed to be almost identical to the values reported for the bulk Ag metal, whereby the Korringa ratio R(= K 2 T 1 T/S) is found to be 2.0 for both samples in the investigated temperature range.

  2. REDOR NMR for Drug Discovery

    PubMed Central

    Cegelski, Lynette

    2014-01-01

    Rotational-Echo DOuble-Resonance (REDOR) NMR is a powerful and versatile solid-state NMR measurement that has been recruited to elucidate drug modes of action and to drive the design of new therapeutics. REDOR has been implemented to examine composition, structure, and dynamics in diverse macromolecular and whole-cell systems, including taxol-bound microtubules, enzyme-cofactor-inhibitor ternary complexes, and antibiotic-whole-cell complexes. The REDOR approach involves the integrated design of specific isotopic labeling strategies and the selection of appropriate REDOR experiments. By way of example, this digest illustrates the versatility of the REDOR approach, with an emphasis on the practical considerations of experimental design and data interpretation. PMID:24035486

  3. NMR Hyperpolarization Techniques for Biomedicine

    PubMed Central

    Nikolaou, Panayiotis; Goodson, Boyd M.

    2015-01-01

    Recent developments in NMR hyperpolarization have enabled a wide array of new in vivo molecular imaging modalities—ranging from functional imaging of the lungs to metabolic imaging of cancer. This Concept article explores selected advances in methods for the preparation and use of hyperpolarized contrast agents, many of which are already at or near the phase of their clinical validation in patients. PMID:25470566

  4. Measurement of deformations by NMR

    NASA Astrophysics Data System (ADS)

    Bytchenkoff, Dimitri; Rodts, Stéphane

    2015-12-01

    Two NMR data acquisition protocols together with corresponding data processing algorithms for locating macroscopic objects, measuring distances between them or monitoring their displacements or deformations with microscopic precision are presented and discussed. The performance of the methods is demonstrated by applying them to the measurement of deformations of a freely supported beam under loading. We believe that our methods will find their applications in mechanics, civil engineering and medicine.

  5. Hyperpolarized 131Xe NMR spectroscopy

    PubMed Central

    Stupic, Karl F.; Cleveland, Zackary I.; Pavlovskaya, Galina E.; Meersmann, Thomas

    2011-01-01

    Hyperpolarized (hp) 131Xe with up to 2.2% spin polarization (i.e., 5000-fold signal enhancement at 9.4 T) was obtained after separation from the rubidium vapor of the spin-exchange optical pumping (SEOP) process. The SEOP was applied for several minutes in a stopped-flow mode, and the fast, quadrupolar-driven T1 relaxation of this spin I = 3/2 noble gas isotope required a rapid subsequent rubidium removal and swift transfer into the high magnetic field region for NMR detection. Because of the xenon density dependent 131Xe quadrupolar relaxation in the gas phase, the SEOP polarization build-up exhibits an even more pronounced dependence on xenon partial pressure than that observed in 129Xe SEOP. 131Xe is the only stable noble gas isotope with a positive gyromagnetic ratio and shows therefore a different relative phase between hp signal and thermal signal compared to all other noble gases. The gas phase 131Xe NMR spectrum displays a surface and magnetic field dependent quadrupolar splitting that was found to have additional gas pressure and gas composition dependence. The splitting was reduced by the presence of water vapor that presumably influences xenon-surface interactions. The hp 131Xe spectrum shows differential line broadening, suggesting the presence of strong adsorption sites. Beyond hp 131Xe NMR spectroscopy studies, a general equation for the high temperature, thermal spin polarization, P, for spin I⩾1/2 nuclei is presented. PMID:21051249

  6. Scalable NMR spectroscopy with semiconductor chips

    PubMed Central

    Ha, Dongwan; Paulsen, Jeffrey; Sun, Nan; Song, Yi-Qiao; Ham, Donhee

    2014-01-01

    State-of-the-art NMR spectrometers using superconducting magnets have enabled, with their ultrafine spectral resolution, the determination of the structure of large molecules such as proteins, which is one of the most profound applications of modern NMR spectroscopy. Many chemical and biotechnological applications, however, involve only small-to-medium size molecules, for which the ultrafine resolution of the bulky, expensive, and high-maintenance NMR spectrometers is not required. For these applications, there is a critical need for portable, affordable, and low-maintenance NMR spectrometers to enable in-field, on-demand, or online applications (e.g., quality control, chemical reaction monitoring) and co-use of NMR with other analytical methods (e.g., chromatography, electrophoresis). As a critical step toward NMR spectrometer miniaturization, small permanent magnets with high field homogeneity have been developed. In contrast, NMR spectrometer electronics capable of modern multidimensional spectroscopy have thus far remained bulky. Complementing the magnet miniaturization, here we integrate the NMR spectrometer electronics into 4-mm2 silicon chips. Furthermore, we perform various multidimensional NMR spectroscopies by operating these spectrometer electronics chips together with a compact permanent magnet. This combination of the spectrometer-electronics-on-a-chip with a permanent magnet represents a useful step toward miniaturization of the overall NMR spectrometer into a portable platform. PMID:25092330

  7. Scalable NMR spectroscopy with semiconductor chips.

    PubMed

    Ha, Dongwan; Paulsen, Jeffrey; Sun, Nan; Song, Yi-Qiao; Ham, Donhee

    2014-08-19

    State-of-the-art NMR spectrometers using superconducting magnets have enabled, with their ultrafine spectral resolution, the determination of the structure of large molecules such as proteins, which is one of the most profound applications of modern NMR spectroscopy. Many chemical and biotechnological applications, however, involve only small-to-medium size molecules, for which the ultrafine resolution of the bulky, expensive, and high-maintenance NMR spectrometers is not required. For these applications, there is a critical need for portable, affordable, and low-maintenance NMR spectrometers to enable in-field, on-demand, or online applications (e.g., quality control, chemical reaction monitoring) and co-use of NMR with other analytical methods (e.g., chromatography, electrophoresis). As a critical step toward NMR spectrometer miniaturization, small permanent magnets with high field homogeneity have been developed. In contrast, NMR spectrometer electronics capable of modern multidimensional spectroscopy have thus far remained bulky. Complementing the magnet miniaturization, here we integrate the NMR spectrometer electronics into 4-mm(2) silicon chips. Furthermore, we perform various multidimensional NMR spectroscopies by operating these spectrometer electronics chips together with a compact permanent magnet. This combination of the spectrometer-electronics-on-a-chip with a permanent magnet represents a useful step toward miniaturization of the overall NMR spectrometer into a portable platform. PMID:25092330

  8. Advanced NMR technology for bioscience and biotechnology

    SciTech Connect

    Hammel, P.C.; Hernandez, G.; Trewhella, J.; Unkefer, C.J.; Boumenthal, D.K.; Kennedy, M.A.; Moore, G.J.

    1998-11-01

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). NMR plays critical roles in bioscience and biotechnology in both imaging and structure determination. NMR is limited, however, by the inherent low sensitivity of the NMR experiment and the demands for spectral resolution required to study biomolecules. The authors addressed both of these issues by working on the development of NMR force microscopy for molecular imaging, and high field NMR with isotope labeling to overcome limitations in the size of biomolecules that can be studied using NMR. A novel rf coil design for NMR force microscopy was developed that increases the limits of sensitivity in magnetic resonance detection for imaging, and the authors demonstrated sub-surface spatial imaging capabilities. The authors also made advances in the miniaturization of two critical NMR force microscope components. They completed high field NMR and isotope labeling studies of a muscle protein complex which is responsible for regulating muscle contraction and is too large for study using conventional NMR approaches.

  9. RpoS synthesis is growth rate regulated in Salmonella typhimurium, but its turnover is not dependent on acetyl phosphate synthesis or PTS function.

    PubMed

    Cunning, C; Elliott, T

    1999-08-01

    The RpoS sigma factor of enteric bacteria is either required for or augments the expression of a number of genes that are induced during nutrient limitation, growth into stationary phase, or in response to stresses, including high osmolarity. RpoS is regulated at multiple levels, including posttranscriptional control of its synthesis, protein turnover, and mechanisms that affect its activity directly. Here, the control of RpoS stability was investigated in Salmonella typhimurium by the isolation of a number of mutants specifically defective in RpoS turnover. These included 20 mutants defective in mviA, the ortholog of Escherichia coli rssB/sprE, and 13 mutants defective in either clpP or clpX which encode the protease active on RpoS. An hns mutant was also defective in RpoS turnover, thus confirming that S. typhimurium and E. coli have identical genetic requirements for this process. Some current models predict the existence of a kinase to phosphorylate the response regulator MviA, but no mutants affecting a kinase were recovered. An mviA mutant carrying the D58N substitution altering the predicted phosphorylation site is substantially defective, suggesting that phosphorylation of MviA on D58 is important for its function. No evidence was obtained to support models in which acetyl phosphate or the PTS system contributes to MviA phosphorylation. However, we did find a significant (fivefold) elevation of RpoS during exponential growth on acetate as the carbon and energy source. This behavior is due to growth rate-dependent regulation which increases RpoS synthesis at slower growth rates. Growth rate regulation operates at the level of RpoS synthesis and is mainly posttranscriptional but, surprisingly, is independent of hfq function. PMID:10438755

  10. Development of LC-13C NMR

    NASA Technical Reports Server (NTRS)

    Dorn, H. C.; Wang, J. S.; Glass, T. E.

    1986-01-01

    This study involves the development of C-13 nuclear resonance as an on-line detector for liquid chromatography (LC-C-13 NMR) for the chemical characterization of aviation fuels. The initial focus of this study was the development of a high sensitivity flow C-13 NMR probe. Since C-13 NMR sensitivity is of paramount concern, considerable effort during the first year was directed at new NMR probe designs. In particular, various toroid coil designs were examined. In addition, corresponding shim coils for correcting the main magnetic field (B sub 0) homogeneity were examined. Based on these initial probe design studies, an LC-C-13 NMR probe was built and flow C-13 NMR data was obtained for a limited number of samples.

  11. Pseudogap in Fe2VGa: NMR evidence

    NASA Astrophysics Data System (ADS)

    Lue, C. S.; Ross, Joseph H.

    2001-02-01

    We report the results of a 51V and 69Ga nuclear magnetic resonance (NMR) study of Fe2VGa at temperatures between 4 and 450 K. The presence of magnetic antisite defects is deduced from the NMR linewidth, which displays a Curie-law temperature dependence. The absence of associated NMR shifts indicates the material to be intrinsically nonmagnetic. At low temperatures the NMR spin-lattice relaxation rate exhibits Korringa behavior, indicating a small carrier density at the Fermi level. At elevated temperatures, the Knight shifts and NMR relaxation rates go over to a thermally activated response, a semiconductor-like behavior. These results are consistent with pseudogap features identified by recent band structure calculations. The Fermi level density of states deduced from NMR is considerably smaller than given by the specific heat coefficient, γ. The electronic properties are compared to the isostructural semimetal Fe2VAl.

  12. Applications of NMR in Dairy Research

    PubMed Central

    Maher, Anthony D.; Rochfort, Simone J.

    2014-01-01

    NMR is a robust analytical technique that has been employed to investigate the properties of many substances of agricultural relevance. NMR was first used to investigate the properties of milk in the 1950s and has since been employed in a wide range of studies; including properties analysis of specific milk proteins to metabolomics techniques used to monitor the health of dairy cows. In this brief review, we highlight the different uses of NMR in the dairy industry. PMID:24958391

  13. Hyphenated low-field NMR techniques: combining NMR with NIR, GPC/SEC and rheometry.

    PubMed

    Räntzsch, Volker; Wilhelm, Manfred; Guthausen, Gisela

    2016-06-01

    Hyphenated low-field NMR techniques are promising characterization methods for online process analytics and comprehensive offline studies of soft materials. By combining different analytical methods with low-field NMR, information on chemical and physical properties can be correlated with molecular dynamics and complementary chemical information. In this review, we present three hyphenated low-field NMR techniques: a combination of near-infrared spectroscopy and time-domain NMR (TD-NMR) relaxometry, online (1) H-NMR spectroscopy measured directly after size exclusion chromatographic (SEC, also known as GPC) separation and a combination of rheometry and TD-NMR relaxometry for highly viscous materials. Case studies are reviewed that underline the possibilities and challenges of the different hyphenated low-field NMR methods. Copyright © 2015 John Wiley & Sons, Ltd. PMID:25854997

  14. Probing surface interactions by combining NMR cryoporometry and NMR relaxometry

    NASA Astrophysics Data System (ADS)

    Mitchell, J.; Stark, S. C.; Strange, J. H.

    2005-06-01

    To further expand on the understanding of surface interactions at the liquid/solid interface on pore walls, the nuclear magnetic resonance (NMR) techniques of cryoporometry and relaxometry have been combined. The combination of these techniques allows variations in NMR relaxation parameters from pore surface to volume ratio changes and from surface interaction changes to be distinguished. By studying a range of sol-gel silicas from two different sources, it was noted that the relaxation time measurements were not consistent with the pore diameters determined by cryoporometry and N2 gas adsorption. Instead distinctly different relaxivity constants were determined for each absorbate in each of the two brands of silica. It was clear that the relaxation times were modified by more than just the pore geometry. Independent experiments on the two brands of silica suggested that the relaxometry results were heavily influenced by the concentration of paramagnetic relaxation centres in the silica gels. The strength of surface interaction, and hence surface affinity, was seen to depend on the liquid in the pores. Using this difference in surface affinities, binary mixtures of alkanes placed in sol-gel silicas were separated via preferential absorption and their components identified using cryoporometry, whereas the components could not be distinguished in the bulk liquid.

  15. Spin-Exchange-Pumped NMR Gyros

    NASA Astrophysics Data System (ADS)

    Walker, T. G.; Larsen, M. S.

    We present the basic theory governing spin-exchange pumped NMR gyros. We review the basic physics of spin-exchange collisions and relaxation as they pertain to precision NMR. We present a simple model of operation as an NMR oscillator and use it to analyze the dynamic response and noise properties of the oscillator. We discuss the primary systematic errors (differential alkali fields, quadrupole shifts, and offset drifts) that limit the bias stability, and discuss methods to minimize them. We give with a brief overview of a practical implementation and performance of an NMR gyro built by Northrop-Grumman Corporation, and conclude with some comments about future prospects.

  16. NMR studies of isotopically labeled RNA

    SciTech Connect

    Pardi, A.

    1994-12-01

    In summary, the ability to generate NMR quantities of {sup 15}N and {sup 13}C-labeled RNAs has led to the development of heteronuclear multi-dimensional NMR techniques for simplifying the resonance assignment and structure determination of RNAs. These methods for synthesizing isotopically labeled RNAs are only several years old, and thus there are still relatively few applications of heteronuclear multi-dimensional NMR techniques to RNA. However, given the critical role that RNAs play in cellular function, one can expect to see an increasing number of NMR structural studies of biologically active RNAs.

  17. Solid-state NMR and Membrane Proteins

    PubMed Central

    Opella, Stanley J.

    2015-01-01

    The native environment for a membrane protein is a phospholipid bilayer. Because the protein is immobilized on NMR timescales by the interactions within a bilayer membrane, solid-state NMR methods are essential to obtain high-resolution spectra. Approaches have been developed for both unoriented and oriented samples, however, they all rest on the foundation of the most fundamental aspects solid-state NMR, and the chemical shift and homo- and hetero-nuclear dipole-dipole interactions. Solid-state NMR has advanced sufficiently to enable the structures of membrane proteins to be determined under near-native conditions in phospholipid bilayers. PMID:25681966

  18. NMR exposure sensitizes tumor cells to apoptosis.

    PubMed

    Ghibelli, L; Cerella, C; Cordisco, S; Clavarino, G; Marazzi, S; De Nicola, M; Nuccitelli, S; D'Alessio, M; Magrini, A; Bergamaschi, A; Guerrisi, V; Porfiri, L M

    2006-03-01

    NMR technology has dramatically contributed to the revolution of image diagnostic. NMR apparatuses use combinations of microwaves over a homogeneous strong (1 Tesla) static magnetic field. We had previously shown that low intensity (0.3-66 mT) static magnetic fields deeply affect apoptosis in a Ca2+ dependent fashion (Fanelli et al., 1999 FASEBJ., 13;95-102). The rationale of the present study is to examine whether exposure to the static magnetic fields of NMR can affect apoptosis induced on reporter tumor cells of haematopoietic origin. The impressive result was the strong increase (1.8-2.5 fold) of damage-induced apoptosis by NMR. This potentiation is due to cytosolic Ca2+ overload consequent to NMR-promoted Ca2+ influx, since it is prevented by intracellular (BAPTA-AM) and extracellular (EGTA) Ca2+ chelation or by inhibition of plasma membrane L-type Ca2+ channels. Three-days follow up of treated cultures shows that NMR decrease long term cell survival, thus increasing the efficiency of cytocidal treatments. Importantly, mononuclear white blood cells are not sensitised to apoptosis by NMR, showing that NMR may increase the differential cytotoxicity of antitumor drugs on tumor vs normal cells. This strong, differential potentiating effect of NMR on tumor cell apoptosis may have important implications, being in fact a possible adjuvant for antitumor therapies. PMID:16528477

  19. Analytical Applications of NMR: Summer Symposium on Analytical Chemistry.

    ERIC Educational Resources Information Center

    Borman, Stuart A.

    1982-01-01

    Highlights a symposium on analytical applications of nuclear magnetic resonance spectroscopy (NMR), discussing pulse Fourier transformation technique, two-dimensional NMR, solid state NMR, and multinuclear NMR. Includes description of ORACLE, an NMR data processing system at Syracuse University using real-time color graphics, and algorithms for…

  20. Access to NMR Spectroscopy for Two-Year College Students: The NMR Site at Trinity University

    ERIC Educational Resources Information Center

    Mills, Nancy S.; Shanklin, Michael

    2011-01-01

    Students at two-year colleges and small four-year colleges have often obtained their exposure to NMR spectroscopy through "canned" spectra because the cost of an NMR spectrometer, particularly a high-field spectrometer, is prohibitive in these environments. This article describes the design of a NMR site at Trinity University in which spectral…

  1. NMR studies of oriented molecules

    SciTech Connect

    Sinton, S.W.

    1981-11-01

    Deuterium and proton magnetic resonance are used in experiments on a number of compounds which either form liquid crystal mesophases themselves or are dissolved in a liquid crystal solvent. Proton multiple quantum NMR is used to simplify complicated spectra. The theory of nonselective multiple quantum NMR is briefly reviewed. Benzene dissolved in a liquid crystal are used to demonstrate several outcomes of the theory. Experimental studies include proton and deuterium single quantum (..delta..M = +-1) and proton multiple quantum spectra of several molecules which contain the biphenyl moiety. 4-Cyano-4'-n-pentyl-d/sub 11/-biphenyl (5CB-d/sub 11/) is studied as a pure compound in the nematic phase. The obtained chain order parameters and dipolar couplings agree closely with previous results. Models for the effective symmetry of the biphenyl group in 5CB-d/sub 11/ are tested against the experimental spectra. The dihedral angle, defined by the planes containing the rings of the biphenyl group, is found to be 30 +- 2/sup 0/ for 5DB-d/sub 11/. Experiments are also described for 4,4'-d/sub 2/-biphenyl, 4,4' - dibromo-biphenyl, and unsubstituted biphenyl.

  2. Picoliter H-1 NMR Spectroscopy

    SciTech Connect

    Minard, Kevin R. ); Wind, Robert A. )

    2002-02-01

    A RF probe that fits inside the bore of a small gradient coil package is described for routine 1H-NMR microscopy measurements on small samples. The probe operates at 500 MHz and houses a 267-um-diameter solenoid transceiver. When used in three dimensional chemical shift imaging (3D-CSI) experiments, the measured signal-to-noise ratio (SNR) is shown to be within 20-30 percent of theoretical limits formulated by only considering the solenoid's resistive losses. This is illustrated using a 100-um-diameter globule of triacylglycerols ({approx}900mM) that may be an oocyte precursor in young Xenopus Laevis frogs, and water sample containing choline at a concentration often found in live cells ({approx}33mM). In chemical shift images generated using a few thousand scans, the choline methyl line is found to have an acceptable SNR in resolved from just 5 picoliters in the Xenopus globule. It is concluded that the probe's sensitivity is sufficient for performing 1H-NMR on picoliter-scale volumes in biological cells and tissues.

  3. NMR Spectroscopy and Its Value: A Primer

    ERIC Educational Resources Information Center

    Veeraraghavan, Sudha

    2008-01-01

    Nuclear magnetic resonance (NMR) spectroscopy is widely used by chemists. Furthermore, the use of NMR spectroscopy to solve structures of macromolecules or to examine protein-ligand interactions is popular. Yet, few students entering graduate education in biological sciences have been introduced to this method or its utility. Over the last six…

  4. An Integrated Laboratory Project in NMR Spectroscopy.

    ERIC Educational Resources Information Center

    Hudson, Reggie L.; Pendley, Bradford D.

    1988-01-01

    Describes an advanced NMR project that can be done with a 60-MHz continuous-wave proton spectrometer. Points out the main purposes are to give students experience in second-order NMR analysis, the simplification of spectra by raising the frequency, and the effect of non-hydrogen nuclei on proton resonances. (MVL)

  5. An Inversion Recovery NMR Kinetics Experiment

    ERIC Educational Resources Information Center

    Williams, Travis J.; Kershaw, Allan D.; Li, Vincent; Wu, Xinping

    2011-01-01

    A convenient laboratory experiment is described in which NMR magnetization transfer by inversion recovery is used to measure the kinetics and thermochemistry of amide bond rotation. The experiment utilizes Varian spectrometers with the VNMRJ 2.3 software, but can be easily adapted to any NMR platform. The procedures and sample data sets in this…

  6. Using Cloud Storage for NMR Data Distribution

    ERIC Educational Resources Information Center

    Soulsby, David

    2012-01-01

    An approach using Google Groups as method for distributing student-acquired NMR data has been implemented. We describe how to configure NMR spectrometer software so that data is uploaded to a laboratory section specific Google Group, thereby removing bottlenecks associated with printing and processing at the spectrometer workstation. Outside of…

  7. A Guided Inquiry Approach to NMR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Parmentier, Laura E.; Lisensky, George C.; Spencer, Brock

    1998-04-01

    We present a novel way to introduce NMR spectroscopy into the general chemistry curriculum as part of a week-long aspirin project in our one-semester introductory course. Aspirin is synthesized by reacting salicylic acid and acetic anhydride. Purity is determined by titration and IR and NMR spectroscopy. Students compare IR and NMR spectra of their aspirin product to a series of reference spectra obtained by the class. Students are able to interpret the IR spectra of their aspirin using IR data from previous experiments. NMR is introduced by having students collect 1H NMR spectra of a series of reference compounds chosen to include some of the structural features of aspirin and compare spectra and structures of the reference compounds to develop a correlation chart for chemical shifts. This process is done in small groups using shared class data and is guided by a series of questions designed to relate the different kinds of hydrogen atoms to number and position of peaks in the NMR spectrum. Students then identify the peaks in the NMR spectrum of their aspirin product and relate percent purity by titration with spectral results and percent yield. This is an enjoyable project that combines the synthesis of a familiar material with a guided inquiry-based introduction to NMR spectroscopy.

  8. Large NMR signals and polarization asymmetries.

    SciTech Connect

    Penttila, S. I.

    1998-11-25

    A large modulation in the series Q-meter can lead to nonlinear NMR signals and asymmetric polarization values. With a careful circuit analysis the nonlinearity can be estimated and corrections to polarization can be determined as a function of the strength of the modulation. We describe the recent LAMPF polarized proton target experiment, its NMR measurement and corrections to the measured polarizations.

  9. Robust, integrated computational control of NMR experiments to achieve optimal assignment by ADAPT-NMR.

    PubMed

    Bahrami, Arash; Tonelli, Marco; Sahu, Sarata C; Singarapu, Kiran K; Eghbalnia, Hamid R; Markley, John L

    2012-01-01

    ADAPT-NMR (Assignment-directed Data collection Algorithm utilizing a Probabilistic Toolkit in NMR) represents a groundbreaking prototype for automated protein structure determination by nuclear magnetic resonance (NMR) spectroscopy. With a [(13)C,(15)N]-labeled protein sample loaded into the NMR spectrometer, ADAPT-NMR delivers complete backbone resonance assignments and secondary structure in an optimal fashion without human intervention. ADAPT-NMR achieves this by implementing a strategy in which the goal of optimal assignment in each step determines the subsequent step by analyzing the current sum of available data. ADAPT-NMR is the first iterative and fully automated approach designed specifically for the optimal assignment of proteins with fast data collection as a byproduct of this goal. ADAPT-NMR evaluates the current spectral information, and uses a goal-directed objective function to select the optimal next data collection step(s) and then directs the NMR spectrometer to collect the selected data set. ADAPT-NMR extracts peak positions from the newly collected data and uses this information in updating the analysis resonance assignments and secondary structure. The goal-directed objective function then defines the next data collection step. The procedure continues until the collected data support comprehensive peak identification, resonance assignments at the desired level of completeness, and protein secondary structure. We present test cases in which ADAPT-NMR achieved results in two days or less that would have taken two months or more by manual approaches. PMID:22427982

  10. NMR and MRI apparatus and method

    DOEpatents

    Clarke, John; Kelso, Nathan; Lee, SeungKyun; Moessle, Michael; Myers, Whittier; McDermott, Robert; ten Haken, Bernard; Pines, Alexander; Trabesinger, Andreas

    2007-03-06

    Nuclear magnetic resonance (NMR) signals are detected in microtesla fields. Prepolarization in millitesla fields is followed by detection with an untuned dc superconducting quantum interference device (SQUID) magnetometer. Because the sensitivity of the SQUID is frequency independent, both signal-to-noise ratio (SNR) and spectral resolution are enhanced by detecting the NMR signal in extremely low magnetic fields, where the NMR lines become very narrow even for grossly inhomogeneous measurement fields. Additional signal to noise benefits are obtained by use of a low noise polarization coil, comprising litz wire or superconducting materials. MRI in ultralow magnetic field is based on the NMR at ultralow fields. Gradient magnetic fields are applied, and images are constructed from the detected NMR signals.

  11. Probing Cancer Cell Metabolism Using NMR Spectroscopy.

    PubMed

    Hollinshead, Kate E R; Williams, Debbie S; Tennant, Daniel A; Ludwig, Christian

    2016-01-01

    Altered cellular metabolism is now accepted to be at the core of many diseases including cancer. Over the past 20 years, NMR has become a core technology to study these metabolic perturbations in detail. This chapter reviews current NMR-based methods for steady-state metabolism and, in particular, the use of non-radioactive stable isotope-enriched tracers. Opportunities and challenges for each method, such as 1D (1)H NMR spectroscopy and (13)C carbon-based NMR spectroscopic methods, are discussed. Ultimately, the combination of NMR and mass spectra as orthogonal technologies are required to compensate for the drawbacks of each technique when used singly are discussed. PMID:27325263

  12. Background suppression in MAS NMR

    NASA Astrophysics Data System (ADS)

    White, Jeffery L.; Beck, Larry W.; Ferguson, David B.; Haw, James F.

    Pulse sequences for suppressing background signals from spinning modules used in magic-angle spinning NMR are described. These pulse sequences are based on spatially selective composite 90° pulses originally reported by Bax, which provide for no net excitation of spins outside the homogeneous region of the coil. We have achieved essentially complete suppression of background signals originating from our Vespel spinning module (which uses a free-standing coil) in both 1H and 13C spectra without notable loss in signal intensity. Successful modification of both Bloch decay and cross-polarization pulse sequences to include spatially selective pulses was essential to acquire background-free spectra for weak samples. Background suppression was also found to be particularly valuable for both T1 and T1 ϱ, relaxation measurements.

  13. NMR solution structure of butantoxin.

    PubMed

    Holaday, S K; Martin, B M; Fletcher, P L; Krishna, N R

    2000-07-01

    The NMR structure of a new toxin, butantoxin (BuTX), which is present in the venoms of the three Brazilian scorpions Tityus serrulatus, Tityus bahiensis, and Tityus stigmurus, has been investigated. This toxin was shown to reversibly block the Shaker B potassium channels (K(d) approximately 660 nM) and inhibit the proliferation of T-cells and the interleukin-2 production of antigen-stimulated T-helper cells. BuTX is a 40 amino acid basic protein stabilized by the four disulfide bridges: Cys2-Cys5, Cys10-Cys31, Cys16-Cys36, and Cys20-Cys38. The latter three are conserved among all members of the short-chain scorpion toxin family, while the first is unique to BuTX. The three-dimensional structure of BuTX was determined using (1)H-NMR spectroscopy. NOESY, phase sensitive COSY (PH-COSY), and amide hydrogen exchange data were used to generate constraints for molecular modeling calculations. Distance geometry and simulated annealing calculations were performed to generate a family of 49 structures free of constraint violations. The secondary structure of BuTX consists of a short 2(1/2) turn alpha-helix (Glu15-Phe23) and a beta-sheet. The beta-sheet is composed of two well-defined antiparallel strands (Gly29-Met32 and Lys35-Cys38) connected by a type-I' beta-turn (Asn33-Asn34). Residues Cys5-Ala9 form a quasi-third strand of the beta-sheet. The N-terminal C2-C5 disulfide bridge unique to this toxin does not appear to confer stability to the protein. PMID:10864437

  14. An Introduction to Biological NMR Spectroscopy*

    PubMed Central

    Marion, Dominique

    2013-01-01

    NMR spectroscopy is a powerful tool for biologists interested in the structure, dynamics, and interactions of biological macromolecules. This review aims at presenting in an accessible manner the requirements and limitations of this technique. As an introduction, the history of NMR will highlight how the method evolved from physics to chemistry and finally to biology over several decades. We then introduce the NMR spectral parameters used in structural biology, namely the chemical shift, the J-coupling, nuclear Overhauser effects, and residual dipolar couplings. Resonance assignment, the required step for any further NMR study, bears a resemblance to jigsaw puzzle strategy. The NMR spectral parameters are then converted into angle and distances and used as input using restrained molecular dynamics to compute a bundle of structures. When interpreting a NMR-derived structure, the biologist has to judge its quality on the basis of the statistics provided. When the 3D structure is a priori known by other means, the molecular interaction with a partner can be mapped by NMR: information on the binding interface as well as on kinetic and thermodynamic constants can be gathered. NMR is suitable to monitor, over a wide range of frequencies, protein fluctuations that play a crucial role in their biological function. In the last section of this review, intrinsically disordered proteins, which have escaped the attention of classical structural biology, are discussed in the perspective of NMR, one of the rare available techniques able to describe structural ensembles. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 16 MCP). PMID:23831612

  15. MAS NMR of HIV-1 protein assemblies

    NASA Astrophysics Data System (ADS)

    Suiter, Christopher L.; Quinn, Caitlin M.; Lu, Manman; Hou, Guangjin; Zhang, Huilan; Polenova, Tatyana

    2015-04-01

    The negative global impact of the AIDS pandemic is well known. In this perspective article, the utility of magic angle spinning (MAS) NMR spectroscopy to answer pressing questions related to the structure and dynamics of HIV-1 protein assemblies is examined. In recent years, MAS NMR has undergone major technological developments enabling studies of large viral assemblies. We discuss some of these evolving methods and technologies and provide a perspective on the current state of MAS NMR as applied to the investigations into structure and dynamics of HIV-1 assemblies of CA capsid protein and of Gag maturation intermediates.

  16. Scalar operators in solid-state NMR

    SciTech Connect

    Sun, Boqin

    1991-11-01

    Selectivity and resolution of solid-state NMR spectra are determined by dispersion of local magnetic fields originating from relaxation effects and orientation-dependent resonant frequencies of spin nuclei. Theoretically, the orientation-dependent resonant frequencies can be represented by a set of irreducible tensors. Among these tensors, only zero rank tensors (scalar operators) are capable of providing high resolution NMR spectra. This thesis presents a series of new developments in high resolution solid-state NMR concerning the reconstruction of various scalar operators motion in solid C{sub 60} is analyzed.

  17. Probing porous media with gas diffusion NMR.

    PubMed

    Mair, R W; Wong, G P; Hoffmann, D; Hurlimann, M D; Patz, S; Schwartz, L M; Walsworth, R L

    1999-10-18

    We show that gas diffusion nuclear magnetic resonance (GD-NMR) provides a powerful technique for probing the structure of porous media. In random packs of glass beads, using both laser-polarized and thermally polarized xenon gas, we find that GD-NMR can accurately measure the pore space surface-area-to-volume ratio, S/V rho, and the tortuosity, alpha (the latter quantity being directly related to the system's transport properties). We also show that GD-NMR provides a good measure of the tortuosity of sandstone and complex carbonate rocks. PMID:11543587

  18. MAS NMR of HIV-1 protein assemblies.

    PubMed

    Suiter, Christopher L; Quinn, Caitlin M; Lu, Manman; Hou, Guangjin; Zhang, Huilan; Polenova, Tatyana

    2015-04-01

    The negative global impact of the AIDS pandemic is well known. In this perspective article, the utility of magic angle spinning (MAS) NMR spectroscopy to answer pressing questions related to the structure and dynamics of HIV-1 protein assemblies is examined. In recent years, MAS NMR has undergone major technological developments enabling studies of large viral assemblies. We discuss some of these evolving methods and technologies and provide a perspective on the current state of MAS NMR as applied to the investigations into structure and dynamics of HIV-1 assemblies of CA capsid protein and of Gag maturation intermediates. PMID:25797001

  19. On electrophoretic NMR. Exploring high conductivity samples

    NASA Astrophysics Data System (ADS)

    Bielejewski, Michał; Giesecke, Marianne; Furó, István

    2014-06-01

    The performance of a new electrophoretic NMR (eNMR) method that uses a Carr-Purcell-Meiboom-Gill echo train with repeated electric field reversal is investigated. We show that this pulse sequence, with acronym CPMGER, yields strongly reduced artifacts from convective flow effects caused by the simultaneous presence of electroosmotic and thermal driving forces. We demonstrate the achieved improvements in various aqueous solutions. Ultimately, the method can be used for obtaining electrophoretic mobilities by eNMR without relying on uncharged reference molecules, otherwise a significant limitation for electrophoretic experiments performed with nuclei other than 1H.

  20. Probing porous media with gas diffusion NMR

    NASA Technical Reports Server (NTRS)

    Mair, R. W.; Wong, G. P.; Hoffmann, D.; Hurlimann, M. D.; Patz, S.; Schwartz, L. M.; Walsworth, R. L.

    1999-01-01

    We show that gas diffusion nuclear magnetic resonance (GD-NMR) provides a powerful technique for probing the structure of porous media. In random packs of glass beads, using both laser-polarized and thermally polarized xenon gas, we find that GD-NMR can accurately measure the pore space surface-area-to-volume ratio, S/V rho, and the tortuosity, alpha (the latter quantity being directly related to the system's transport properties). We also show that GD-NMR provides a good measure of the tortuosity of sandstone and complex carbonate rocks.

  1. NMR data handbook for biomedical applications

    SciTech Connect

    Beall, P.T.; Amtey, S.R.; Kasturi, S.R.

    1984-01-01

    The text is divided into 10 chapters, each of which covers a specific block of material and has its own references. The volume is meant to serve as a laboratory handbook and a desk reference, containing basic NMR theory, useful formulae and physical constants, and compiled data from the NMR literature. The volume attempts to cover the development of biological NMR through several decades of in vitro experiments that have laid the groundwork for and pointed to profitable areas of investigation for new in vivo techniques.

  2. NMR Analysis of Unknowns: An Introduction to 2D NMR Spectroscopy

    ERIC Educational Resources Information Center

    Alonso, David E.; Warren, Steven E.

    2005-01-01

    A study combined 1D (one-dimensional) and 2D (two-dimensional) NMR spectroscopy to solve structural organic problems of three unknowns, which include 2-, 3-, and 4-heptanone. Results showed [to the first power]H NMR and [to the thirteenth power]C NMR signal assignments for 2- and 3-heptanone were more challenging than for 4-heptanone owing to the…

  3. NMR Methods to Study Dynamic Allostery

    PubMed Central

    Grutsch, Sarina; Brüschweiler, Sven; Tollinger, Martin

    2016-01-01

    Nuclear magnetic resonance (NMR) spectroscopy provides a unique toolbox of experimental probes for studying dynamic processes on a wide range of timescales, ranging from picoseconds to milliseconds and beyond. Along with NMR hardware developments, recent methodological advancements have enabled the characterization of allosteric proteins at unprecedented detail, revealing intriguing aspects of allosteric mechanisms and increasing the proportion of the conformational ensemble that can be observed by experiment. Here, we present an overview of NMR spectroscopic methods for characterizing equilibrium fluctuations in free and bound states of allosteric proteins that have been most influential in the field. By combining NMR experimental approaches with molecular simulations, atomistic-level descriptions of the mechanisms by which allosteric phenomena take place are now within reach. PMID:26964042

  4. Epitope mapping by solution NMR spectroscopy.

    PubMed

    Bardelli, M; Livoti, E; Simonelli, L; Pedotti, M; Moraes, A; Valente, A P; Varani, L

    2015-06-01

    Antibodies play an ever more prominent role in basic research as well as in the biotechnology and pharmaceutical sectors. Characterizing their epitopes, that is, the region that they recognize on their target molecule, is useful for purposes ranging from molecular biology research to vaccine design and intellectual property protection. Solution NMR spectroscopy is ideally suited to the atomic level characterization of intermolecular interfaces and, as a consequence, to epitope discovery. Here, we illustrate how NMR epitope mapping can be used to rapidly and accurately determine protein antigen epitopes. The basic concept is that differences in the NMR signal of an antigen free or bound by an antibody will identify epitope residues. NMR epitope mapping provides more detailed information than mutagenesis or peptide mapping and can be much more rapid than X-ray crystallography. Advantages and drawbacks of this technique are discussed together with practical considerations. PMID:25726811

  5. Quantitative analysis of NMR spectra with chemometrics

    NASA Astrophysics Data System (ADS)

    Winning, H.; Larsen, F. H.; Bro, R.; Engelsen, S. B.

    2008-01-01

    The number of applications of chemometrics to series of NMR spectra is rapidly increasing due to an emerging interest for quantitative NMR spectroscopy e.g. in the pharmaceutical and food industries. This paper gives an analysis of advantages and limitations of applying the two most common chemometric procedures, Principal Component Analysis (PCA) and Multivariate Curve Resolution (MCR), to a designed set of 231 simple alcohol mixture (propanol, butanol and pentanol) 1H 400 MHz spectra. The study clearly demonstrates that the major advantage of chemometrics is the visualisation of larger data structures which adds a new exploratory dimension to NMR research. While robustness and powerful data visualisation and exploration are the main qualities of the PCA method, the study demonstrates that the bilinear MCR method is an even more powerful method for resolving pure component NMR spectra from mixtures when certain conditions are met.

  6. A New Microcell Technique for NMR Analysis.

    ERIC Educational Resources Information Center

    Yu, Sophia J.

    1987-01-01

    Describes a new laboratory technique for working with small samples of compounds used in nuclear magnetic resonance (NMR) analysis. Demonstrates how microcells can be constructed for each experiment and samples can be recycled. (TW)

  7. NMR and optical studies of piezoelectric polymers

    SciTech Connect

    Schmidt, V.H.; Tuthill, G.F.

    1993-01-01

    Progress is reported in several areas dealing with piezoelectric (electroactive) polymers (mostly vinylidene fluoride, trifluoroethylene, copolymers, PVF[sub 2]) and liquid crystals. Optical studies, neutron scattering, NMR, thermal, theory and modeling were done.

  8. NMR-Assisted Molecular Docking Methodologies.

    PubMed

    Sturlese, Mattia; Bellanda, Massimo; Moro, Stefano

    2015-08-01

    Nuclear magnetic resonance (NMR) spectroscopy and molecular docking are regularly being employed as helpful tools of drug discovery research. Molecular docking is an extremely rapid method to evaluate possible binders from a large chemical library in a fast and cheap manner. NMR techniques can directly detect a protein-ligand interaction, can determine the corresponding association constant, and can consistently identify the ligand binding cavity. Consequently, molecular docking and NMR techniques are naturally complementary techniques where the combination of the two has the potential to improve the overall efficiency of drug discovery process. In this review, we would like to summarize the state of the art of docking methods which have been recently bridged to NMR experiments to identify novel and effective therapeutic drug candidates. PMID:27490497

  9. Interfaces in polymer nanocomposites - An NMR study

    NASA Astrophysics Data System (ADS)

    Böhme, Ute; Scheler, Ulrich

    2016-03-01

    Nuclear Magnetic Resonance (NMR) is applied for the investigation of polymer nanocomposites. Solid-state NMR is applied to study the modification steps to compatibilize layered double hydroxides with non-polar polymers. 1H relaxation NMR gives insight on the polymer dynamics over a wide range of correlation times. For the polymer chain dynamics the transverse relaxation time T2 is most suited. In this presentation we report on two applications of T2 measurements under external mechanical stress. In a low-field system relaxation NMR studies are performed in-situ under uniaxial stress. High-temperature experiments in a Couette cell permit the investigation of the polymer dynamics in the melt under shear flow.

  10. Rheology of Blood by NMR

    NASA Astrophysics Data System (ADS)

    Han, Song-I.; Marseille, Oliver; Gehlen, Christa; Blümich, Bernhard

    2001-09-01

    Pipe flow of blood in tubes of 1 and 7 mm inner diameter, respectively, was investigated employing two-dimensional NMR velocity imaging and PFG propagator measurements at different Reynolds numbers between 10 and 3500. The results are compared to flow of a water/glycerol mixture of matching viscosity under identical conditions. The transition from laminar to turbulent flow is observed by both a flattening of the velocity profile and a change of the propagator shape. For blood flow this transition is found to be shifted toward higher Reynolds numbers as compared to the transition of the water/glycerol mixture. This observation is in agreement with predictions from hydraulic measurements and is a consequence of the non-Newtonian flow characteristics of blood as a suspension of erythrocytes and plasma. Likewise, a deviation from the laminar flow condition is observed for blood at low Reynolds numbers between 10 and 100. This phenomenon is unknown for Newtonian liquids and is explained by the onset of a geometrical arrangement of the erythrocytes, the so-called rouleaux effect.

  11. Rheology of blood by NMR.

    PubMed

    Han, S I; Marseille, O; Gehlen, C; Blümich, B

    2001-09-01

    Pipe flow of blood in tubes of 1 and 7 mm inner diameter, respectively, was investigated employing two-dimensional NMR velocity imaging and PFG propagator measurements at different Reynolds numbers between 10 and 3500. The results are compared to flow of a water/glycerol mixture of matching viscosity under identical conditions. The transition from laminar to turbulent flow is observed by both a flattening of the velocity profile and a change of the propagator shape. For blood flow this transition is found to be shifted toward higher Reynolds numbers as compared to the transition of the water/glycerol mixture. This observation is in agreement with predictions from hydraulic measurements and is a consequence of the non-Newtonian flow characteristics of blood as a suspension of erythrocytes and plasma. Likewise, a deviation from the laminar flow condition is observed for blood at low Reynolds numbers between 10 and 100. This phenomenon is unknown for Newtonian liquids and is explained by the onset of a geometrical arrangement of the erythrocytes, the so-called rouleaux effect. PMID:11531367

  12. Technical Letter Report Development of Flaw Size Distribution Tables Including Effects of Flaw Depth Sizing Errors for Draft 10CFR 50.61a (Alternate PTS Rule) JCN-N6398, Task 4

    SciTech Connect

    Simonen, Fredric A.; Gosselin, Stephen R.; Doctor, Steven R.

    2013-04-22

    This document describes a new method to determine whether the flaws in a particular reactor pressure vessel are consistent with the assumptions regarding the number and sizes of flaws used in the analyses that formed the technical justification basis for the new voluntary alternative Pressurized Thermal Shock (PTS) rule (Draft 10 CFR 50.61a). The new methodology addresses concerns regarding prior methodology because ASME Code Section XI examinations do not detect all fabrication flaws, they have higher detection performance for some flaw types, and there are flaw sizing errors always present (e.g., significant oversizing of small flaws and systematic under sizing of larger flaws). The new methodology allows direct comparison of ASME Code Section XI examination results with values in the PTS draft rule Tables 2 and 3 in order to determine if the number and sizes of flaws detected by an ASME Code Section XI examination are consistent with those assumed in the probabilistic fracture mechanics calculations performed in support of the development of 10 CFR 50.61a.

  13. PAS7 encodes a novel yeast member of the WD-40 protein family essential for import of 3-oxoacyl-CoA thiolase, a PTS2-containing protein, into peroxisomes.

    PubMed Central

    Marzioch, M; Erdmann, R; Veenhuis, M; Kunau, W H

    1994-01-01

    To identify components of the peroxisomal import pathway in yeast, we have isolated pas mutants affected in peroxisome biogenesis. Two mutants assigned to complementation group 7 define a new gene, PAS7, whose product is necessary for import of thiolase, a PTS2-containing protein, but not for that of SKL (PTS1)-containing proteins, into peroxisomes. We have cloned PAS7 by complementation of the oleic acid non-utilizing phenotype of the pas7-1 strain. The DNA sequence predicts a 42.3 kDa polypeptide of 375 amino acids encoding a novel member of the beta-transducin related (WD-40) protein family. A Myc epitope-tagged Pas7p, expressed under the control of the CUP1 promotor, was functionally active. Subcellular localization studies revealed that in the presence of thiolase this epitope-tagged Pas7p in part associates with peroxisomes. However, in a thiolase-deficient mutant, Pas7p was entirely found in the cytoplasm. We suggest that Pas7p mediates the binding of thiolase to these organelles. Images PMID:7957058

  14. Modern NMR spectroscopy: a guide for chemists

    SciTech Connect

    Sanders, J.K.M.; Hunter, B.K.

    1988-01-01

    The aim of the authors of Modern NMR Spectroscopy is to bridge the communication gap between the chemist and the spectroscopist. The approach is nonmathematical, descriptive, and pictorial. To illustrate the ideas introduced in the text, the authors provide original spectra obtained specially for this purpose. Examples include spectroscopy of protons, carbon, and less receptive nuclei of interest to inorganic chemists. The authors succeed in making high-resolution NMR spectroscopy comprehensible for the average student or chemist.

  15. Frontiers of NMR in Molecular Biology

    SciTech Connect

    1999-08-25

    NMR spectroscopy is expanding the horizons of structural biology by determining the structures and describing the dynamics of blobular proteins in aqueous solution, as well as other classes of proteins including membrane proteins and the polypeptides that form the aggregates diagnostic of prion and amyloid diseases. Significant results are also emerging on DNA and RNA oligomers and their complexes with proteins. This meeting focused attention on key structural questions emanating from molecular biology and how NMR spectroscopy can be used to answer them.

  16. NMR of Membrane Proteins: Beyond Crystals.

    PubMed

    Rajesh, Sundaresan; Overduin, Michael; Bonev, Boyan B

    2016-01-01

    Membrane proteins are essential for the flow of signals, nutrients and energy between cells and between compartments of the cell. Their mechanisms can only be fully understood once the precise structures, dynamics and interactions involved are defined at atomic resolution. Through advances in solution and solid state NMR spectroscopy, this information is now available, as demonstrated by recent studies of stable peripheral and transmembrane proteins. Here we highlight recent cases of G-protein coupled receptors, outer membrane proteins, such as VDAC, phosphoinositide sensors, such as the FAPP-1 pleckstrin homology domain, and enzymes including the metalloproteinase MMP-12. The studies highlighted have resulted in the determination of the 3D structures, dynamical properties and interaction surfaces for membrane-associated proteins using advanced isotope labelling strategies, solubilisation systems and NMR experiments designed for very high field magnets. Solid state NMR offers further insights into the structure and multimeric assembly of membrane proteins in lipid bilayers, as well as into interactions with ligands and targets. Remaining challenges for wider application of NMR to membrane structural biology include the need for overexpression and purification systems for the production of isotope-labelled proteins with fragile folds, and the availability of only a few expensive perdeuterated detergents.Step changes that may transform the field include polymers, such as styrene maleic acid, which obviate the need for detergent altogether, and allow direct high yield purification from cells or membranes. Broader demand for NMR may be facilitated by MODA software, which instantly predicts membrane interactive residues that can subsequently be validated by NMR. In addition, recent developments in dynamic nuclear polarization NMR instrumentation offer a remarkable sensitivity enhancement from low molarity samples and cell surfaces. These advances illustrate the current

  17. NMR studies of multiphase flows II

    SciTech Connect

    Altobelli, S.A.; Caprihan, A.; Fukushima, E.

    1995-12-31

    NMR techniques for measurements of spatial distribution of material phase, velocity and velocity fluctuation are being developed and refined. Versions of these techniques which provide time average liquid fraction and fluid phase velocity have been applied to several concentrated suspension systems which will not be discussed extensively here. Technical developments required to further extend the use of NMR to the multi-phase flow arena and to provide measurements of previously unobtainable parameters are the focus of this report.

  18. NEMS - National Energy Modeling System: An Overview

    EIA Publications

    2009-01-01

    The National Energy Modeling System: An Overview 2009 a summary description of NEMS and each of its components. NEMS is a computer-based, energy-economy modeling system of energy markets for the midterm period through 2030. The NEMS is used to produce the Annual Energy Outlook.

  19. Multidimensional NMR spectroscopy in a single scan.

    PubMed

    Gal, Maayan; Frydman, Lucio

    2015-11-01

    Multidimensional NMR has become one of the most widespread spectroscopic tools available to study diverse structural and functional aspects of organic and biomolecules. A main feature of multidimensional NMR is the relatively long acquisition times that these experiments demand. For decades, scientists have been working on a variety of alternatives that would enable NMR to overcome this limitation, and deliver its data in shorter acquisition times. Counting among these methodologies is the so-called ultrafast (UF) NMR approach, which in principle allows one to collect arbitrary multidimensional correlations in a single sub-second transient. By contrast to conventional acquisitions, a main feature of UF NMR is a spatiotemporal manipulation of the spins that imprints the chemical shift and/or J-coupling evolutions being sought, into a spatial pattern. Subsequent gradient-based manipulations enable the reading out of this information and its multidimensional correlation into patterns that are identical to those afforded by conventional techniques. The current review focuses on the fundamental principles of this spatiotemporal UF NMR manipulation, and on a few of the methodological extensions that this form of spectroscopy has undergone during the years. PMID:26249041

  20. 33S NMR cryogenic probe for taurine detection

    NASA Astrophysics Data System (ADS)

    Hobo, Fumio; Takahashi, Masato; Maeda, Hideaki

    2009-03-01

    With the goal of a S33 nuclear magnetic resonance (NMR) probe applicable to in vivo NMR on taurine-biological samples, we have developed the S33 NMR cryogenic probe, which is applicable to taurine solutions. The NMR sensitivity gain relative to a conventional broadband probe is as large as 3.5. This work suggests that improvements in the preamplifier could allow NMR measurements on 100 μM taurine solutions, which is the level of sensitivity necessary for biological samples.

  1. Sensitivity of nonuniform sampling NMR.

    PubMed

    Palmer, Melissa R; Suiter, Christopher L; Henry, Geneive E; Rovnyak, James; Hoch, Jeffrey C; Polenova, Tatyana; Rovnyak, David

    2015-06-01

    Many information-rich multidimensional experiments in nuclear magnetic resonance spectroscopy can benefit from a signal-to-noise ratio (SNR) enhancement of up to about 2-fold if a decaying signal in an indirect dimension is sampled with nonconsecutive increments, termed nonuniform sampling (NUS). This work provides formal theoretical results and applications to resolve major questions about the scope of the NUS enhancement. First, we introduce the NUS Sensitivity Theorem in which any decreasing sampling density applied to any exponentially decaying signal always results in higher sensitivity (SNR per square root of measurement time) than uniform sampling (US). Several cases will illustrate this theorem and show that even conservative applications of NUS improve sensitivity by useful amounts. Next, we turn to a serious limitation of uniform sampling: the SNR by US decreases for extending evolution times, and thus total experimental times, beyond 1.26T2 (T2 = signal decay constant). Thus, SNR and resolution cannot be simultaneously improved by extending US beyond 1.26T2. We find that NUS can eliminate this constraint, and we introduce the matched NUS SNR Theorem: an exponential sampling density matched to the signal decay always improves the SNR with additional evolution time. Though proved for a specific case, broader classes of NUS densities also improve SNR with evolution time. Applications of these theoretical results are given for a soluble plant natural product and a solid tripeptide (u-(13)C,(15)N-MLF). These formal results clearly demonstrate the inadequacies of applying US to decaying signals in indirect nD-NMR dimensions, supporting a broader adoption of NUS. PMID:25901905

  2. Use of NMR and NMR Prediction Software to Identify Components in Red Bull Energy Drinks

    ERIC Educational Resources Information Center

    Simpson, Andre J.; Shirzadi, Azadeh; Burrow, Timothy E.; Dicks, Andrew P.; Lefebvre, Brent; Corrin, Tricia

    2009-01-01

    A laboratory experiment designed as part of an upper-level undergraduate analytical chemistry course is described. Students investigate two popular soft drinks (Red Bull Energy Drink and sugar-free Red Bull Energy Drink) by NMR spectroscopy. With assistance of modern NMR prediction software they identify and quantify major components in each…

  3. Nuclear magnetic resonance apparatus having semitoroidal rf coil for use in topical NMR and NMR imaging

    DOEpatents

    Fukushima, Eiichi; Roeder, Stephen B. W.; Assink, Roger A.; Gibson, Atholl A. V.

    1986-01-01

    An improved nuclear magnetic resonance (NMR) apparatus for use in topical magnetic resonance (TMR) spectroscopy and other remote sensing NMR applications includes a semitoroidal radio-frequency (rf) coil. The semitoroidal rf coil produces an effective alternating magnetic field at a distance from the poles of the coil, so as to enable NMR measurements to be taken from selected regions inside an object, particularly including human and other living subjects. The semitoroidal rf coil is relatively insensitive to magnetic interference from metallic objects located behind the coil, thereby rendering the coil particularly suited for use in both conventional and superconducting NMR magnets. The semitoroidal NMR coil can be constructed so that it emits little or no excess rf electric field associated with the rf magnetic field, thus avoiding adverse effects due to dielectric heating of the sample or to any other interaction of the electric field with the sample.

  4. Calibration of NMR well logs from carbonate reservoirs with laboratory NMR measurements and μXRCT

    SciTech Connect

    Mason, Harris E.; Smith, Megan M.; Hao, Yue; Carroll, Susan A.

    2014-12-31

    The use of nuclear magnetic resonance (NMR) well log data has the potential to provide in-situ porosity, pore size distributions, and permeability of target carbonate CO₂ storage reservoirs. However, these methods which have been successfully applied to sandstones have yet to be completely validated for carbonate reservoirs. Here, we have taken an approach to validate NMR measurements of carbonate rock cores with independent measurements of permeability and pore surface area to volume (S/V) distributions using differential pressure measurements and micro X-ray computed tomography (μXRCT) imaging methods, respectively. We observe that using standard methods for determining permeability from NMR data incorrectly predicts these values by orders of magnitude. However, we do observe promise that NMR measurements provide reasonable estimates of pore S/V distributions, and with further independent measurements of the carbonate rock properties that universally applicable relationships between NMR measured properties may be developed for in-situ well logging applications of carbonate reservoirs.

  5. BOOK REVIEW: NMR Imaging of Materials

    NASA Astrophysics Data System (ADS)

    Blümich, Bernhard

    2003-09-01

    Magnetic resonance imaging (MRI) of materials is a field of increasing importance. Applications extend from fundamental science like the characterization of fluid transport in porous rock, catalyst pellets and hemodialysers into various fields of engineering for process optimization and product quality control. While the results of MRI imaging are being appreciated by a growing community, the methods of imaging are far more diverse for materials applications than for medical imaging of human beings. Blümich has delivered the first book in this field. It was published in hardback three years ago and is now offered as a paperback for nearly half the price. The text provides an introduction to MRI imaging of materials covering solid-state NMR spectroscopy, imaging methods for liquid and solid samples, and unusual MRI in terms of specialized approaches to spatial resolution such as an MRI surface scanner. The book represents an excellent and thorough treatment which will help to grow research in materials MRI. Blümich developed the treatise over many years for his research students, graduates in chemistry, physics and engineering. But it may also be useful for medical students looking for a less formal discussion of solid-state NMR spectroscopy. The structure of this book is easy to perceive. The first three chapters cover an introduction, the fundamentals and methods of solid-state NMR spectroscopy. The book starts at the ground level where no previous knowledge about NMR is assumed. Chapter 4 discusses a wide variety of transformations beyond the Fourier transformation. In particular, the Hadamard transformation and the 'wavelet' transformation are missing from most related books. This chapter also includes a description of noise-correlation spectroscopy, which promises the imaging of large objects without the need for extremely powerful radio-frequency transmitters. Chapters 5 and 6 cover basic imaging methods. The following chapter about the use of relaxation and

  6. NMR techniques in the study of cardiovascular structure and functions

    SciTech Connect

    Osbakken, M.; Haselgrove, J.

    1987-01-01

    The chapter titles of this book are: Introduction to NMR Techniques;Theory of NMR Probe Design;Overview of Magnetic Resonance Imaging to Study the Cardiovascular System;Vascular Anatomy and Physiology Studied with NMR Techniques;Assessment of Myocardial Ischemia and Infarction by Nuclear Magnetic Resonance Imaging;The Use of MRI in Congenital Heart Disease;Cardiomyopathies and Myocarditis Studied with NMR Techniques;Determination of Myocardial Mechanical Function with Magnetic Resonance Imaging Techniques;Determination of Flow Using NMR Techniques;The Use of Contrast Agents in Cardiac MRI;Can Cardiovascular Disease Be Effectively Evaluated with NMR Spectroscopy. NMR Studies of ATP Synthesis Reactions in the Isolated Heart;Studies of Intermediary Metabolism in the Heart by 13C NMR Spectroscopy;23Na and 39K NMR Spectroscopic Studies of the Intact Beating Heart;and Evaluation of Skeletal Muscle Metabolism in Patients with Congestive Heart Failure Using Phosphorus Nuclear Magnetic Resonance.

  7. NMR studies of cation transport across membranes

    SciTech Connect

    Shochet, N.R.

    1985-01-01

    /sup 23/Na NMR Studies of cation transport across membranes were conducted both on model and biological membranes. Two ionophores, the carrier monensin and the channel-former gramicidin, were chosen to induce cation transport in large unilamellar phosphatidylcholine vesicles. The distinction between the NMR signals arising from the two sides of the membrane was achieved by the addition of an anionic paramagnetic shift reagent to the outer solution. The kinetics of the cation transport across the membrane was observed simultaneously monitoring the changes in the /sup 23/Na NMR signals of both compartments. Two mathematical models were developed for the estimation of the transport parameters of the monensin- and gramicidin-induced cation transport. The models were able to fit the experimental data very well. A new method for the estimation of the volume trapped inside the vesicles was developed. The method uses the relative areas of the intra- and extravesicular NMR signals arising from a suspension of vesicles bathed in the same medium they contain, as a measure for the relative volumes of these compartments. Sodium transport across biological membranes was studied by /sup 23/ NMR, using suspensions of cultured nerve cells. The sodium influx through voltage-gated channels was studied using the channel modifier batrachotoxin in combination with scorpion toxin.

  8. Theoretical NMR correlations based Structure Discussion

    PubMed Central

    2011-01-01

    The constitutional assignment of natural products by NMR spectroscopy is usually based on 2D NMR experiments like COSY, HSQC, and HMBC. The actual difficulty of the structure elucidation problem depends more on the type of the investigated molecule than on its size. The moment HMBC data is involved in the process or a large number of heteroatoms is present, a possibility of multiple solutions fitting the same data set exists. A structure elucidation software can be used to find such alternative constitutional assignments and help in the discussion in order to find the correct solution. But this is rarely done. This article describes the use of theoretical NMR correlation data in the structure elucidation process with WEBCOCON, not for the initial constitutional assignments, but to define how well a suggested molecule could have been described by NMR correlation data. The results of this analysis can be used to decide on further steps needed to assure the correctness of the structural assignment. As first step the analysis of the deviation of carbon chemical shifts is performed, comparing chemical shifts predicted for each possible solution with the experimental data. The application of this technique to three well known compounds is shown. Using NMR correlation data alone for the description of the constitutions is not always enough, even when including 13C chemical shift prediction. PMID:21797997

  9. NMR structural studies on antifreeze proteins.

    PubMed

    Sönnichsen, F D; Davies, P L; Sykes, B D

    1998-01-01

    Antifreeze proteins (AFPs) are a structurally diverse class of proteins that bind to ice and inhibit its growth in a noncolligative manner. This adsorption-inhibition mechanism operating at the ice surface results in a lowering of the (nonequilibrium) freezing point below the melting point. A lowering of approximately 1 degree C, which is sufficient to prevent fish from freezing in ice-laden seawater, requires millimolar AFP levels in the blood. The solubility of AFPs at these millimolar concentrations and the small size of the AFPs (typically 3-15 kDa) make them ideal subjects for NMR analysis. Although fish AFPs are naturally abundant, seasonal expression, restricted access to polar fishes, and difficulties in separating numerous similar isoforms have made protein expression the method of choice for producing AFPs for structural studies. Expression of recombinant AFPs has also facilitated NMR analysis by permitting isotopic labeling with 15N and 13C and has permitted mutations to be made to help with the interpretation of NMR data. NMR analysis has recently solved two AFP structures and provided valuable information about the disposition of ice-binding side chains in a third. The potential exists to solve other AFP structures, including the newly described insect AFPs, and to use solid-state NMR techniques to address fundamental questions about the nature of the interaction between AFPs and ice. PMID:9923697

  10. The CANDU Reactor System: An Appropriate Technology.

    PubMed

    Robertson, J A

    1978-02-10

    CANDU power reactors are characterized by the combination of heavy water as moderator and pressure tubes to contain the fuel and coolant. Their excellent neutron economy provides the simplicity and low costs of once-through natural-uranium fueling. Future benefits include the prospect of a near-breeder thorium fuel cycle to provide security of fuel supply without the need to develop a new reactor such as the fast breeder. These and other features make the CANDU system an appropriate technology for countries, like Canada, of intermediate economic and industrial capacity. PMID:17788102

  11. Wide-line NMR and protein hydration.

    PubMed

    Tompa, K; Bokor, M; Tompa, P

    2012-01-01

    In this chapter, the reader is introduced to the basics of wide-line NMR, with particular focus on the following: (1) basic theoretical and experimental NMR elements, necessary before switching the spectrometer and designing the experiment, (2) models/theories for the interpretation of measured data, (3) definition of wide-line NMR spectrometry, the description of the measurement and evaluation variants, useful hints for the novice, (4) advice on selecting the solvent, which is not a trivial task, (5) a note of warning that not all data are acceptable in spite of the statistical confidence. Finally, we wrap up the chapter with the results on two proteins (a globular and an intrinsically disordered). PMID:22760320

  12. Remote tuning of NMR probe circuits.

    PubMed

    Kodibagkar, V D; Conradi, M S

    2000-05-01

    There are many circumstances in which the probe tuning adjustments cannot be located near the rf NMR coil. These may occur in high-temperature NMR, low-temperature NMR, and in the use of magnets with small diameter access bores. We address here circuitry for connecting a fixed-tuned probe circuit by a transmission line to a remotely located tuning network. In particular, the bandwidth over which the probe may be remotely tuned while keeping the losses in the transmission line acceptably low is considered. The results show that for all resonant circuit geometries (series, parallel, series-parallel), overcoupling of the line to the tuned circuit is key to obtaining a large tuning bandwidth. At equivalent extents of overcoupling, all resonant circuit geometries have nearly equal remote tuning bandwidths. Particularly for the case of low-loss transmission line, the tuning bandwidth can be many times the tuned circuit's bandwidth, f(o)/Q. PMID:10783273

  13. Review of NMR characterization of pyrolysis oils

    DOE PAGESBeta

    Hao, Naijia; Ben, Haoxi; Yoo, Chang Geun; Adhikari, Sushil; Ragauskas, Arthur J.

    2016-08-24

    Here, pyrolysis of renewable biomass has been developed as a method to produce green fuels and chemicals in response to energy security concerns as well as to alleviate environmental issues incurred with fossil fuel usage. However, pyrolysis oils still have limited commercial application, mainly because unprocessed oils cannot be readily blended with current petroleum-based transportation fuels. To better understand these challenges, researchers have applied diverse characterization techniques in the development of bio-oil studies. In particular, nuclear magnetic resonance (NMR) is a key spectroscopic characterization method through analysis of bio-oil components. This review highlights the NMR strategies for pyrolysis oil characterizationmore » and critically discusses the applications of 1H, 13C, 31P, 19F, and two-dimensional (2-D NMR) analyses such as heteronuclear single quantum correlation (HSQC) in representative pyrolysis oil studies.« less

  14. A modularized pulse programmer for NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Mao, Wenping; Bao, Qingjia; Yang, Liang; Chen, Yiqun; Liu, Chaoyang; Qiu, Jianqing; Ye, Chaohui

    2011-02-01

    A modularized pulse programmer for a NMR spectrometer is described. It consists of a networked PCI-104 single-board computer and a field programmable gate array (FPGA). The PCI-104 is dedicated to translate the pulse sequence elements from the host computer into 48-bit binary words and download these words to the FPGA, while the FPGA functions as a sequencer to execute these binary words. High-resolution NMR spectra obtained on a home-built spectrometer with four pulse programmers working concurrently demonstrate the effectiveness of the pulse programmer. Advantages of the module include (1) once designed it can be duplicated and used to construct a scalable NMR/MRI system with multiple transmitter and receiver channels, (2) it is a totally programmable system in which all specific applications are determined by software, and (3) it provides enough reserve for possible new pulse sequences.

  15. An NMR Study of Microvoids in Polymers

    NASA Technical Reports Server (NTRS)

    Toy, James; Mattrix, Larry

    1996-01-01

    An understanding of polymer defect structures, like microvoids in polymeric matrices, is most crucial to their fabrication and application potential. In this project guest atoms are introduced into the microvoids in PMR-15 and NMR is used to determine microvoid sizes and locations. Xenon is a relatively inert probe that would normally not be found naturally in polymer or in NMR probe materials. There are two NMR active Xenon isotopes, Xe-129 and Xe-131. The Xe atom has a very high polarizability, which makes it sensitive to the intracrystalline environment of polymers. Interactions between the Xe atoms and the host matrix perturb and Xe electron cloud, deshielding the nuclei, and thereby expanding the range of the observed NMR chemical shifts. This chemical shift range which may be as large as 5000 ppm, permits subtle structural and chemical effects to be studied with high sensitivity. The Xe-129-NMR line shape has been found to vary in response to changes in the pore symmetry of the framework hosts in Zeolites and Clathrasil compounds. Before exposure to Xe gas, the PMR-15 samples were dried in a vacuum oven at 150 C for 48 hours. The samples were then exposed to Xe gas at 30 psi for 72 hours and sealed in glass tubes with 1 atmosphere of Xenon gas. Xenon gas at 1 atmosphere was used to tune up the spectrometer and to set up the appropriate NMR parameters. A series of spectra were obtained interspersed with applications of vacuum and heating to drive out the adsorbed Xe and determine the role of Xe-Xe interactions in the observed chemical shift.

  16. Hyperpolarized Xenon for NMR and MRI Applications

    PubMed Central

    Witte, Christopher; Kunth, Martin; Döpfert, Jörg; Rossella, Federica; Schröder, Leif

    2012-01-01

    Nuclear magnetic resonance (NMR) spectroscopy and imaging (MRI) suffer from intrinsic low sensitivity because even strong external magnetic fields of ~10 T generate only a small detectable net-magnetization of the sample at room temperature 1. Hence, most NMR and MRI applications rely on the detection of molecules at relative high concentration (e.g., water for imaging of biological tissue) or require excessive acquisition times. This limits our ability to exploit the very useful molecular specificity of NMR signals for many biochemical and medical applications. However, novel approaches have emerged in the past few years: Manipulation of the detected spin species prior to detection inside the NMR/MRI magnet can dramatically increase the magnetization and therefore allows detection of molecules at much lower concentration 2. Here, we present a method for polarization of a xenon gas mixture (2-5% Xe, 10% N2, He balance) in a compact setup with a ca. 16000-fold signal enhancement. Modern line-narrowed diode lasers allow efficient polarization 7 and immediate use of gas mixture even if the noble gas is not separated from the other components. The SEOP apparatus is explained and determination of the achieved spin polarization is demonstrated for performance control of the method. The hyperpolarized gas can be used for void space imaging, including gas flow imaging or diffusion studies at the interfaces with other materials 8,9. Moreover, the Xe NMR signal is extremely sensitive to its molecular environment 6. This enables the option to use it as an NMR/MRI contrast agent when dissolved in aqueous solution with functionalized molecular hosts that temporarily trap the gas 10,11. Direct detection and high-sensitivity indirect detection of such constructs is demonstrated in both spectroscopic and imaging mode. PMID:22986346

  17. Development of an in Situ NMR Photoreactor To Study Environmental Photochemistry.

    PubMed

    Bliumkin, Liora; Dutta Majumdar, Rudraksha; Soong, Ronald; Adamo, Antonio; Abbatt, Jonathan P D; Zhao, Ran; Reiner, Eric; Simpson, André J

    2016-06-01

    Photochemistry is a key environmental process directly linked to the fate, source, and toxicity of pollutants in the environment. This study explores two approaches for integrating light sources with nuclear magnetic resonance (NMR) spectroscopy: sample irradiation using a "sunlight simulator" outside the magnet versus direct irradiation of the sample inside the magnet. To assess their applicability, the in situ NMR photoreactors were applied to a series of environmental systems: an atmospheric pollutant (p-nitrophenol), crude oil extracts, and groundwater. The study successfully illustrates that environmentally relevant aqueous photochemical processes can be monitored in situ and in real time using NMR spectroscopy. A range of intermediates and degradation products were identified and matched to the literature. Preliminary measurements of half-lives were also obtained from kinetic curves. The sunlight simulator was shown to be the most suitable model to explore environmental photolytic processes in situ. Other light sources with more intense UV output hold potential for evaluating UV as a remediation alternative in areas such as wastewater treatment plants or oil spills. Finally, the ability to analyze the photolytic fate of trace chemicals at natural abundance in groundwater, using a cryogenic probe, demonstrates the viability of NMR spectroscopy as a powerful and complementary technique for environmental applications in general. PMID:27172272

  18. An optical NMR spectrometer for Larmor-beat detection and high-resolution POWER NMR

    NASA Astrophysics Data System (ADS)

    Kempf, J. G.; Marohn, J. A.; Carson, P. J.; Shykind, D. A.; Hwang, J. Y.; Miller, M. A.; Weitekamp, D. P.

    2008-06-01

    Optical nuclear magnetic resonance (ONMR) is a powerful probe of electronic properties in III-V semiconductors. Larmor-beat detection (LBD) is a sensitivity optimized, time-domain NMR version of optical detection based on the Hanle effect. Combining LBD ONMR with the line-narrowing method of POWER (perturbations observed with enhanced resolution) NMR further enables atomically detailed views of local electronic features in III-Vs. POWER NMR spectra display the distribution of resonance shifts or line splittings introduced by a perturbation, such as optical excitation or application of an electric field, that is synchronized with a NMR multiple-pulse time-suspension sequence. Meanwhile, ONMR provides the requisite sensitivity and spatial selectivity to isolate local signals within macroscopic samples. Optical NMR, LBD, and the POWER method each introduce unique demands on instrumentation. Here, we detail the design and implementation of our system, including cryogenic, optical, and radio-frequency components. The result is a flexible, low-cost system with important applications in semiconductor electronics and spin physics. We also demonstrate the performance of our systems with high-resolution ONMR spectra of an epitaxial AlGaAs /GaAs heterojunction. NMR linewidths down to 4.1Hz full width at half maximum were obtained, a 103-fold resolution enhancement relative any previous optically detected NMR experiment.

  19. 13C NMR Metabolomics: INADEQUATE Network Analysis

    PubMed Central

    Clendinen, Chaevien S.; Pasquel, Christian; Ajredini, Ramadan; Edison, Arthur S.

    2015-01-01

    The many advantages of 13C NMR are often overshadowed by its intrinsically low sensitivity. Given that carbon makes up the backbone of most biologically relevant molecules, 13C NMR offers a straightforward measurement of these compounds. Two-dimensional 13C-13C correlation experiments like INADEQUATE (incredible natural abundance double quantum transfer experiment) are ideal for the structural elucidation of natural products and have great but untapped potential for metabolomics analysis. We demonstrate a new and semi-automated approach called INETA (INADEQUATE network analysis) for the untargeted analysis of INADEQUATE datasets using an in silico INADEQUATE database. We demonstrate this approach using isotopically labeled Caenorhabditis elegans mixtures. PMID:25932900

  20. 14 N NMR of tetrapropylammonium based crystals

    NASA Astrophysics Data System (ADS)

    Dib, E.; Mineva, T.; Gaveau, P.; Alonso, B.

    2015-07-01

    We have investigated using 14N NMR different types of materials containing tetrapropylammonium cations. We consider the tetrapropylammonium bromide crystal as well as two different microporous materials silicalite-1 and AlPO-5, with MFI and AFI topology respectively, where the tetrapropylammonium cation plays the role of structure directing agent. 14N NMR quadrupolar coupling parameters were determined experimentally for all the crystals. In addition calculations based on Density Functional Theory with empirical dispersion (DFT-D) were performed on the MFI type zeolite. The sensitivity of the 14N quadrupolar coupling parameters to the spatial distribution of the anions in the zeolite's framework is emphasized.

  1. 1H NMR relaxation in urea

    NASA Astrophysics Data System (ADS)

    Taylor, R. E.; Bacher, Alfred D.; Dybowski, C.

    2007-11-01

    Proton NMR spin-lattice relaxation times T1 were measured for urea as a function of temperature. An activation energy of 46.3 ± 4.7 kJ/mol was extracted and compared with the range of 38-65 kJ/mol previously reported in the literature as measured by different magnetic resonance techniques. In addition, proton NMR spin-lattice relaxation times in the rotating frame T1 ρ were measured as a function of temperature. These measurements provide acquisition conditions for the 13C and 15N CP/MAS spectra of pure urea in the crystalline phase.

  2. Tritiation methods and tritium NMR spectroscopy

    SciTech Connect

    Jaiswal, D.K.; Morimoto, H.; Salijoughian, M.; Williams, P.G.

    1991-09-01

    We have used a simple process for the production of highly tritiated water and characterized the product species by {sup 1}H and {sup 3}H NMR spectroscopy. The water is readily manipulated and used in subsequent reactions either as T{sub 2}O, CH{sub 3}COOT or CF{sub 3}COOT. Development of tritiated diimide has progressed to the point where cis-hydrogenated products at 1-20 Ci/mmole S.A. are possible. Tri-n-butyl tin tritide has been produced at >95% tritium content and well characterized by multinuclear NMR techniques. 27 refs., 3 figs.

  3. NMR investigation of the quantum pigeonhole effect

    NASA Astrophysics Data System (ADS)

    V. S., Anjusha; Hegde, Swathi S.; Mahesh, T. S.

    2016-02-01

    NMR quantum simulators have been used for studying various quantum phenomena. Here, using a four-qubit NMR quantum simulator, we investigate the recently postulated quantum pigeonhole effect. In this phenomenon, a set of three particles in a two-path interferometer often appears to be in such a superposition that no two particles can be assigned a single path, thus exhibiting the nonclassical behavior. In our experiments, quantum pigeons are emulated by three nuclear qubits whose states are probed jointly and noninvasively by an ancillary spin. The experimental results are in good agreement with quantum theoretical predictions.

  4. NMR Microscopy - Micron-Level Resolution.

    NASA Astrophysics Data System (ADS)

    Kwok, Wing-Chi Edmund

    1990-01-01

    Nuclear Magnetic Resonance Imaging (MRI) has been developed into a powerful and widely used diagnostic tool since the invention of techniques using linear magnetic field gradients in 1973. The variety of imaging contrasts obtainable in MRI, such as spin density, relaxation times and flow rate, gives MRI a significant advantage over other imaging techniques. For common diagnostic applications, image resolutions have been in the order of millimeters with slice thicknesses in centimeters. For many research applications, however, resolutions in the order of tens of microns or smaller are needed. NMR Imaging in these high resolution disciplines is known as NMR microscopy. Compared with conventional microscopy, NMR microscopy has the advantage of being non-invasive and non-destructive. The major obstacles of NMR microscopy are low signal-to-noise ratio and effects due to spin diffusion. To overcome these difficulties, more sensitive RF probes and very high magnetic field gradients have to be used. The most effective way to increase sensitivity is to build smaller probes. Microscope probes of different designs have been built and evaluated. Magnetic field gradient coils that can produce linear field gradients up to 450 Gauss/cm were also assembled. In addition, since microscope probes often employ remote capacitors for RF tuning, the associated signal loss in the transmission line was studied. Imaging experiments have been carried out in a 2.1 Tesla small bore superconducting magnet using the typical two-dimensional spin warp imaging technique. Images have been acquired for both biological and non-biological samples. The highest resolution was obtained in an image of a nerve bundle from the spinal cord of a racoon and has an in-plane resolution of 4 microns. These experiments have demonstrated the potential application of NMR microscopy to pathological research, nervous system study and non -destructive testings of materials. One way to further improve NMR microscopy is

  5. Magic Angle Spinning NMR of Viruses

    PubMed Central

    Quinn, Caitlin; Lu, Manman; Suiter, Christopher L.; Hou, Guangjin; Zhang, Huilan; Polenova, Tatyana

    2015-01-01

    Viruses, relatively simple pathogens, are able to replicate in many living organisms and to adapt to various environments. Conventional atomic-resolution structural biology techniques, X-ray crystallography and solution NMR spectroscopy provided abundant information on the structures of individual proteins and nucleic acids comprising viruses; however, viral assemblies are not amenable to analysis by these techniques because of their large size, insolubility, and inherent lack of long-range order. In this article, we review the recent advances in magic angle spinning NMR spectroscopy that enabled atomic-resolution analysis of structure and dynamics of large viral systems and give examples of several exciting case studies. PMID:25919197

  6. Sensitive detection of NMR for thin films.

    PubMed

    Lee, Soonchil

    2015-10-01

    NMR can provide valuable information about thin films, but its relatively low sensitivity allows data acquisition only from bulk samples. The sensitivity problem is circumvented by detection schemes with higher sensitivity and/or enhanced polarization. In most of these ingenious techniques, electrons play a central role through hyperfine interactions with the nuclei of interest or the conversion of the spin orientation to an electric charge. The state of the art in NMR is the control of a single nuclear spin state, the complete form of which is one of the ultimate goals of nanotechnology. PMID:26549846

  7. The Quiet Renaissance of Protein NMR

    PubMed Central

    Barrett, Paul J.; Chen, Jiang; Cho, Min-Kyu; Kim, Ji-Hun; Lu, Zhenwei; Mathew, Sijo; Peng, Dungeng; Song, Yuanli; Van Horn, Wade D.; Zhuang, Tiandi; Sönnichsen, Frank D.; Sanders, Charles R.

    2013-01-01

    From roughly 1985 through the start of the new millennium, the cutting edge of solution protein nuclear magnetic resonance (NMR) spectroscopy was to a significant extent driven by the aspiration to determine structures. Here we survey recent advances in protein NMR that herald a renaissance in which a number of its most important applications reflect the broad problem-solving capability displayed by this method during its classical era during the 1970s and early 80s. “Without receivers fitted and kept in order, the air may tingle and thrill with the message, but it will not reach my spirit and consciousness.” Mary Slessor, Calabar, circa 1910 PMID:23368985

  8. NMR Stark Spectroscopy: New Methods to Calibrate NMR Sensitivity to Electric Fields

    NASA Astrophysics Data System (ADS)

    Tarasek, Matthew R.

    The influence of electrostatics on NMR parameters is well accepted. Thus, NMR is a promising route to probe electrical features within molecules and materials. However, applications of NMR Stark effects (E-field induced changes in spin energy levels) have been elusive. I have developed new approaches to resolve NMR Stark effects from an applied E field. This calibrates nuclear probes whose spectral response might later be used to evaluate internal E fields that are critical to function, such as those due to local charge distributions or sample structure. I will present two novel experimental approaches for direct calibration of NMR quadrupolar Stark effects (QSEs). In the first, steady-state (few-second) excitation by an E field at twice the NMR frequency (2ω 0) is used to saturate spin magnetization. The extent of saturation vs. E-field amplitude calibrates the QSE response rate, while measurements vs sample orientation determine tensorial character. The second method instead synchronizes short (few µs) pulses of the 2ω0 E field with a multiple-pulse NMR sequence. This, “POWER” (Perturbations Observed With Enhanced Resolution) approach enables more accurate measure of small QSEs (i.e. few Hz spectral changes). A 2nd key advantage is the ability to define tensorial response without reorienting the sample, but instead varying the phase of the 2ω0 field. I will describe these experiments and my home-built NMR “Stark probe”, employed on a conventional wide-bore solid-state NMR system. Results with GaAs demonstrate each method, while extensions to a wider array of molecular and material systems may now be possible using these methods.

  9. Solid-state NMR imaging system

    DOEpatents

    Gopalsami, Nachappa; Dieckman, Stephen L.; Ellingson, William A.

    1992-01-01

    An apparatus for use with a solid-state NMR spectrometer includes a special imaging probe with linear, high-field strength gradient fields and high-power broadband RF coils using a back projection method for data acquisition and image reconstruction, and a real-time pulse programmer adaptable for use by a conventional computer for complex high speed pulse sequences.

  10. Hyperpolarized NMR Probes for Biological Assays

    PubMed Central

    Meier, Sebastian; Jensen, Pernille R.; Karlsson, Magnus; Lerche, Mathilde H.

    2014-01-01

    During the last decade, the development of nuclear spin polarization enhanced (hyperpolarized) molecular probes has opened up new opportunities for studying the inner workings of living cells in real time. The hyperpolarized probes are produced ex situ, introduced into biological systems and detected with high sensitivity and contrast against background signals using high resolution NMR spectroscopy. A variety of natural, derivatized and designed hyperpolarized probes has emerged for diverse biological studies including assays of intracellular reaction progression, pathway kinetics, probe uptake and export, pH, redox state, reactive oxygen species, ion concentrations, drug efficacy or oncogenic signaling. These probes are readily used directly under natural conditions in biofluids and are often directly developed and optimized for cellular assays, thus leaving little doubt about their specificity and utility under biologically relevant conditions. Hyperpolarized molecular probes for biological NMR spectroscopy enable the unbiased detection of complex processes by virtue of the high spectral resolution, structural specificity and quantifiability of NMR signals. Here, we provide a survey of strategies used for the selection, design and use of hyperpolarized NMR probes in biological assays, and describe current limitations and developments. PMID:24441771

  11. A Primer of Fourier Transform NMR.

    ERIC Educational Resources Information Center

    Macomber, Roger S.

    1985-01-01

    Fourier transform nuclear magnetic resonance (NMR) is a new spectroscopic technique that is often omitted from undergraduate curricula because of lack of instructional materials. Therefore, information is provided to introduce students to the technique of data collection and transformation into the frequency domain. (JN)

  12. Solid-state NMR for bacterial biofilms

    NASA Astrophysics Data System (ADS)

    Reichhardt, Courtney; Cegelski, Lynette

    2014-04-01

    Bacteria associate with surfaces and one another by elaborating an extracellular matrix to encapsulate cells, creating communities termed biofilms. Biofilms are beneficial in some ecological niches, but also contribute to the pathogenesis of serious and chronic infectious diseases. New approaches and quantitative measurements are needed to define the composition and architecture of bacterial biofilms to help drive the development of strategies to interfere with biofilm assembly. Solid-state nuclear magnetic resonance (NMR) is uniquely suited to the examination of insoluble and complex macromolecular and whole-cell systems. This article highlights three examples that implement solid-state NMR to deliver insights into bacterial biofilm composition and changes in cell-wall composition as cells transition to the biofilm lifestyle. Most recently, solid-state NMR measurements provided a total accounting of the protein and polysaccharide components in the extracellular matrix of an Escherichia coli biofilm and transformed our qualitative descriptions of matrix composition into chemical parameters that permit quantitative comparisons among samples. We present additional data for whole biofilm samples (cells plus the extracellular matrix) that complement matrix-only analyses. The study of bacterial biofilms by solid-state NMR is an exciting avenue ripe with many opportunities and we close the article by articulating some outstanding questions and future directions in this area.

  13. Solid-state NMR imaging system

    SciTech Connect

    Gopalsami, N.; Dieckman, S.L.; Ellingson, W.A.

    1990-01-01

    An accessory for use with a solid-state NMR spectrometer includes a special imaging probe with linear, high-field strength gradient fields and high-power broadband RF coils using a back projection method for data acquisition and image reconstruction, and a real-time pulse programmer adaptable for use by a conventional computer for complex high speed pulse sequences.

  14. Structural Studies of Biological Solids Using NMR

    NASA Astrophysics Data System (ADS)

    Ramamoorthy, Ayyalusamy

    2011-03-01

    High-resolution structure and dynamics of biological molecules are important in understanding their function. While studies have been successful in solving the structures of water-soluble biomolecules, it has been proven difficult to determine the structures of membrane proteins and fibril systems. Recent studies have shown that solid-state NMR is a promising technique and could be highly valuable in studying such non-crystalline and non-soluble biosystems. I will present strategies to study the structures of such challenging systems and also about the applications of solid-state NMR to study the modes of membrane-peptide interactions for a better assessment of the prospects of antimicrobial peptides as substitutes to antibiotics in the control of human disease. Our studies on the mechanism of membrane disruption by LL-37 (a human antimicrobial peptide), analogs of the naturally occurring antimicrobial peptide magainin2 extracted from the skin of the African frog Xenopus Laevis, and pardaxin will be presented. Solid-state NMR experiments were used to determine the secondary structure, dynamics and topology of these peptides in lipid bilayers. Similarities and difference in the cell-lysing mechanism, and their dependence on the membrane composition, of these peptides will be discussed. Atomic-level resolution NMR structures of amyloidogenic proteins revealing the misfolding pathway and early intermediates that play key roles in amyloid toxicity will also be presented.

  15. Increasing the quantitative bandwidth of NMR measurements.

    PubMed

    Power, J E; Foroozandeh, M; Adams, R W; Nilsson, M; Coombes, S R; Phillips, A R; Morris, G A

    2016-02-18

    The frequency range of quantitative NMR is increased from tens to hundreds of kHz by a new pulse sequence, CHORUS. It uses chirp pulses to excite uniformly over very large bandwidths, yielding accurate integrals even for nuclei such as (19)F that have very wide spectra. PMID:26789115

  16. NMR analysis of a fluorocarbon copolymer

    SciTech Connect

    Smith, R.E.; Smith, C.H.

    1987-10-01

    Vinylidene fluoride (VF/sub 2/) can be copolymerized with chlorotrifluoroethylene (CTFE) in an aqueous emulsion using a peroxide chain initiator. The physical properties of the resulting fluorocarbon polymer depend on the ratio of VF/sub 2/ to CTFE and the randomness of the copolymerization. When CTFE and VF are polymerized in an approximately 3:1 mole ratio, the resulting polymer is soluble in acetone (and other solvents) at room temperature. Using proton and fluorine-19 NMR, the mole ratio of CTFE to VF/sub 2/, the emulsifier (perfluorodecanoate) concentration, and the randomness of copolymerization can be determined. A trifluorotoluene internal standard is added to a d/sub 6/-acetone solution of the fluoropolymer. Proton NMR is used to determine the amount of VF/sub 2/. Fluorine-19 NMR is used to measure the amount of emulsifier and the randomness of copolymerization. Each analysis requires about 5 minutes, and is quite precise, with relative standard deviations from 3 to 10% (10 replicates analyzed). In addition, the results from NMR analyses agree well with wet chemical analyses. 4 refs., 3 figs., 3 tabs.

  17. SQUID detected NMR in microtesla magnetic fields

    NASA Astrophysics Data System (ADS)

    Matlachov, Andrei N.; Volegov, Petr L.; Espy, Michelle A.; George, John S.; Kraus, Robert H.

    2004-09-01

    We have built an NMR system that employs a superconducting quantum interference device (SQUID) detector and operates in measurement fields of 2-25 μT. The system uses a pre-polarizing field from 4 to 30 mT generated by simple room-temperature wire-wound coils that are turned off during measurements. The instrument has an open geometry with samples located outside the cryostat at room-temperature. This removes constraints on sample size and allows us to obtain signals from living tissue. We have obtained 1H NMR spectra from a variety of samples including water, mineral oil, and a live frog. We also acquired gradient encoded free induction decay (FID) data from a water-plastic phantom in the μT regime, from which simple projection images were reconstructed. NMR signals from samples inside metallic containers have also been acquired. This is possible because the penetration skin depth is much greater at the low operating frequencies of this system than for conventional systems. Advantages to ultra-low field NMR measurements include lower susceptibility artifacts caused by high strength polarizing and measurement fields, and negligible line width broadening due to measurement field inhomogeneity, reducing the burden of producing highly homogeneous fields.

  18. Advanced Laboratory NMR Spectrometer with Applications.

    ERIC Educational Resources Information Center

    Biscegli, Clovis; And Others

    1982-01-01

    A description is given of an inexpensive nuclear magnetic resonance (NMR) spectrometer suitable for use in advanced laboratory courses. Applications to the nondestructive analysis of the oil content in corn seeds and in monitoring the crystallization of polymers are presented. (SK)

  19. Combining solid-state NMR spectroscopy with first-principles calculations - a guide to NMR crystallography.

    PubMed

    Ashbrook, Sharon E; McKay, David

    2016-06-01

    Recent advances in the application of first-principles calculations of NMR parameters to periodic systems have resulted in widespread interest in their use to support experimental measurement. Such calculations often play an important role in the emerging field of "NMR crystallography", where NMR spectroscopy is combined with techniques such as diffraction, to aid structure determination. Here, we discuss the current state-of-the-art for combining experiment and calculation in NMR spectroscopy, considering the basic theory behind the computational approaches and their practical application. We consider the issues associated with geometry optimisation and how the effects of temperature may be included in the calculation. The automated prediction of structural candidates and the treatment of disordered and dynamic solids are discussed. Finally, we consider the areas where further development is needed in this field and its potential future impact. PMID:27117884

  20. An NMR study of microvoids in polymers

    NASA Technical Reports Server (NTRS)

    Toy, James; Mattix, Larry

    1995-01-01

    An understanding of polymer defect structures, like microvoids in polymeric matrices, is crucial to their fabrication and application potential. In this project guest atoms are introduced into the microvoids in PMR-15 and NMR is used to determine microvoid sizes and locations. Xenon is a relatively inert probe that would normally be found naturally in polymer or in NMR probe materials. There are two NMR active xenon isotopes, Xe-129 and Xe-131. The Xe atom has a very high polarizability, which makes it sensitive to the intracrystalline environment of polymers. Interactions between the Xe atoms and the host matrix perturb the Xe electron cloud, deshielding the nuclei, and thereby expanding the range of the observed NMR chemical shifts. This chemical shift range which may be as large as 5000 ppm, permits subtle structural and chemical effects to be studied with high sensitivity. The Xe(129)-NMR line shape has been found to vary in response to changes in the pore symmetry of the framework hosts line Zeolites and Clathrasil compounds. Before exposure to Xe gas, the PMR-15 samples were dried in a vacuum oven at 150 C for 48 hours. The samples were then exposed to Xe gas at 30 psi for 72 hours and sealed in glass tubes with 1 atmosphere of xenon gas. Xenon gas at 1 atmosphere was used to tune up the spectrometer and to set up the appropriate NMR parameters. A single Xe-129 line at 83.003498 Mhz (with protons at 300 Mhz) was observed for the gas. With the xenon charged PMR-15 samples, a second broader line is observed 190 ppm downfield from the gas line (also observed). The width of the NMR line from the Xe-129 absorbed in the polymer is at least partially due to the distribution of microvoid sizes. From the chemical shift (relative to the gas line) and the line width, we estimate the average void sizes to be 2.74 +/- 0.20 angstroms. Since Xe-129 has such a large chemical shift range (approximately 5000 ppm), we expect the chemical shift anisotropy to contribute to the

  1. Superoxygenated Water as an Experimental Sample for NMR Relaxometry

    ERIC Educational Resources Information Center

    Nestle, Nikolaus; Dakkouri, Marwan; Rauscher, Hubert

    2004-01-01

    The increase in NMR relaxation rates as a result of dissolved paramagnetic species on the sample of superoxygenated drinking water is demonstrated. It is concluded that oxygen content in NMR samples is an important issue and can give rise to various problems in the interpretation of both spectroscopic and NMR imaging or relaxation experiments.

  2. Applications of Diffusion Ordered Spectroscopy (DOSY-NMR)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Diffusion-ordered NMR (DOSY-NMR) is a powerful, but under-utilized, technique for the investigation of mixtures based on translational diffusion rates. DOSY spectra allow for determination by NMR of components that may differ in molecular weight, geometry or complexation. Typical applications coul...

  3. Solid-state NMR studies of supercapacitors.

    PubMed

    Griffin, John M; Forse, Alexander C; Grey, Clare P

    2016-01-01

    Electrochemical double-layer capacitors, or 'supercapacitors' are attracting increasing attention as high-power energy storage devices for a wide range of technological applications. These devices store charge through electrostatic interactions between liquid electrolyte ions and the surfaces of porous carbon electrodes. However, many aspects of the fundamental mechanism of supercapacitance are still not well understood, and there is a lack of experimental techniques which are capable of studying working devices. Recently, solid-state NMR has emerged as a powerful tool for studying the local environments and behaviour of electrolyte ions in supercapacitor electrodes. In this Trends article, we review these recent developments and applications. We first discuss the basic principles underlying the mechanism of supercapacitance, as well as the key NMR observables that are relevant to the study of supercapacitor electrodes. We then review some practical aspects of the study of working devices using ex situ and in situ methodologies and explain the key advances that these techniques have allowed on the study of supercapacitor charging mechanisms. NMR experiments have revealed that the pores of the carbon electrodes contain a significant number of electrolyte ions in the absence of any charging potential. This has important implications for the molecular mechanisms of supercapacitance, as charge can be stored by different ion adsorption/desorption processes. Crucially, we show how in situ NMR experiments can be used to quantitatively study and characterise the charging mechanism, with the experiments providing the most detailed picture of charge storage to date, offering the opportunity to design enhanced devices. Finally, an outlook for future directions for solid-state NMR in supercapacitor research is offered. PMID:26974032

  4. NMR Constraints Analyser: a web-server for the graphical analysis of NMR experimental constraints.

    PubMed

    Heller, Davide Martin; Giorgetti, Alejandro

    2010-07-01

    Nuclear magnetic resonance (NMR) spectroscopy together with X-ray crystallography, are the main techniques used for the determination of high-resolution 3D structures of biological molecules. The output of an NMR experiment includes a set of lower and upper limits for the distances (constraints) between pairs of atoms. If the number of constraints is high enough, there will be a finite number of possible conformations (models) of the macromolecule satisfying the data. Thus, the more constraints are measured, the better defined these structures will be. The availability of a user-friendly tool able to help in the analysis and interpretation of the number of experimental constraints per residue, is thus of valuable importance when assessing the levels of structure definition of NMR solved biological macromolecules, in particular, when high-quality structures are needed in techniques such as, computational biology approaches, site-directed mutagenesis experiments and/or drug design. Here, we present a free publicly available web-server, i.e. NMR Constraints Analyser, which is aimed at providing an automatic graphical analysis of the NMR experimental constraints atom by atom. The NMR Constraints Analyser server is available from the web-page http://molsim.sci.univr.it/constraint. PMID:20513646

  5. OPENCORE NMR: open-source core modules for implementing an integrated FPGA-based NMR spectrometer.

    PubMed

    Takeda, Kazuyuki

    2008-06-01

    A tool kit for implementing an integrated FPGA-based NMR spectrometer [K. Takeda, A highly integrated FPGA-based nuclear magnetic resonance spectrometer, Rev. Sci. Instrum. 78 (2007) 033103], referred to as the OPENCORE NMR spectrometer, is open to public. The system is composed of an FPGA chip and several peripheral boards for USB communication, direct-digital synthesis (DDS), RF transmission, signal acquisition, etc. Inside the FPGA chip have been implemented a number of digital modules including three pulse programmers, the digital part of DDS, a digital quadrature demodulator, dual digital low-pass filters, and a PC interface. These FPGA core modules are written in VHDL, and their source codes are available on our website. This work aims at providing sufficient information with which one can, given some facility in circuit board manufacturing, reproduce the OPENCORE NMR spectrometer presented here. Also, the users are encouraged to modify the design of spectrometer according to their own specific needs. A home-built NMR spectrometer can serve complementary roles to a sophisticated commercial spectrometer, should one comes across such new ideas that require heavy modification to hardware inside the spectrometer. This work can lower the barrier of building a handmade NMR spectrometer in the laboratory, and promote novel and exciting NMR experiments. PMID:18374613

  6. Squid detected NMR and MRI at ultralow fields

    SciTech Connect

    Clarke, John; McDermott, Robert; Pines, Alexander; Trabesinger, Andreas Heinz

    2007-05-15

    Nuclear magnetic resonance (NMR) signals are detected in microtesla fields. Prepolarization in millitesla fields is followed by detection with an untuned dc superconducting quantum interference device (SQUID) magnetometer. Because the sensitivity of the SQUID is frequency independent, both signal-to-noise ratio (SNR) and spectral resolution are enhanced by detecting the NMR signal in extremely low magnetic fields, where the NMR lines become very narrow even for grossly inhomogeneous measurement fields. MRI in ultralow magnetic field is based on the NMR at ultralow fields. Gradient magnetic fields are applied, and images are constructed from the detected NMR signals.

  7. Squid detected NMR and MRI at ultralow fields

    DOEpatents

    Clarke, John; McDermott, Robert; Pines, Alexander; Trabesinger, Andreas Heinz

    2006-05-30

    Nuclear magnetic resonance (NMR) signals are detected in microtesla fields. Prepolarization in millitesla fields is followed by detection with an untuned dc superconducting quantum interference device (SQUID) magnetometer. Because the sensitivity of the SQUID is frequency independent, both signal-to-noise ratio (SNR) and spectral resolution are enhanced by detecting the NMR signal in extremely low magnetic fields, where the NMR lines become very narrow even for grossly inhomogeneous measurement fields. MRI in ultralow magnetic field is based on the NMR at ultralow fields. Gradient magnetic fields are applied, and images are constructed from the detected NMR signals.

  8. SQUID detected NMR and MRI at ultralow fields

    DOEpatents

    Clarke, John; McDermott, Robert; Pines, Alexander; Trabesinger, Andreas Heinz

    2006-10-03

    Nuclear magnetic resonance (NMR) signals are detected in microtesla fields. Prepolarization in millitesla fields is followed by detection with an untuned dc superconducting quantum interference device (SQUID) magnetometer. Because the sensitivity of the SQUID is frequency independent, both signal-to-noise ratio (SNR) and spectral resolution are enhanced by detecting the NMR signal in extremely low magnetic fields, where the NMR lines become very narrow even for grossly inhomogeneous measurement fields. MRI in ultralow magnetic field is based on the NMR at ultralow fields. Gradient magnetic fields are applied, and images are constructed from the detected NMR signals.

  9. Squid detected NMR and MRI at ultralow fields

    SciTech Connect

    Clarke, John; Pines, Alexander; McDermott, Robert F.; Trabesinger, Andreas H.

    2008-12-16

    Nuclear magnetic resonance (NMR) signals are detected in microtesla fields. Prepolarization in millitesla fields is followed by detection with an untuned dc superconducting quantum interference device (SQUID) magnetometer. Because the sensitivity of the SQUID is frequency independent, both signal-to-noise ratio (SNR) and spectral resolution are enhanced by detecting the NMR signal in extremely low magnetic fields, where the NMR lines become very narrow even for grossly inhomogeneous measurement fields. MRI in ultralow magnetic field is based on the NMR at ultralow fields. Gradient magnetic fields are applied, and images are constructed from the detected NMR signals.

  10. NMR CHARACTERIZATIONS OF PROPERTIES OF HETEROGENEOUS MEDIA

    SciTech Connect

    C.T. Philip Chang; Changho Choi; Jeromy T. Hollenshead; Rudi Michalak; Jack Phan; Ramon Saavedra; John C. Slattery; Jinsoo Uh; Randi Valestrand; A. Ted Watson; Song Xue

    2005-01-01

    A critical and long-standing need within the petroleum industry is the specification of suitable petrophysical properties for mathematical simulation of fluid flow in petroleum reservoirs (i.e., reservoir characterization). The development of accurate reservoir characterizations is extremely challenging. Property variations may be described on many scales, and the information available from measurements reflect different scales. In fact, experiments on laboratory core samples, well-log data, well-test data, and reservoir-production data all represent information potentially valuable to reservoir characterization, yet they all reflect information about spatial variations of properties at different scales. Nuclear magnetic resonance (NMR) spectroscopy and imaging (MRI) provide enormous potential for developing new descriptions and understandings of heterogeneous media. NMR has the rare capability to probe permeable media non-invasively, with spatial resolution, and it provides unique information about molecular motions and interactions that are sensitive to morphology. NMR well-logging provides the best opportunity ever to resolve permeability distributions within petroleum reservoirs. We develop MRI methods to determine, for the first time, spatially resolved distributions of porosity and permeability within permeable media samples that approach the intrinsic scale: the finest resolution of these macroscopic properties possible. To our knowledge, this is the first time that the permeability is actually resolved at a scale smaller than the sample. In order to do this, we have developed a robust method to determine of relaxation distributions from NMR experiments and a novel implementation and analysis of MRI experiments to determine the amount of fluid corresponding to imaging regions, which are in turn used to determine porosity and saturation distributions. We have developed a novel MRI experiment to determine velocity distributions within flowing experiments, and

  11. Sodium ion effect on silk fibroin conformation characterized by solid-state NMR and generalized 2D NMR NMR correlation

    NASA Astrophysics Data System (ADS)

    Ruan, Qing-Xia; Zhou, Ping

    2008-07-01

    In the present work, we investigated Na + ion effect on the silk fibroin (SF) conformation. Samples are Na +-involved regenerated silk fibroin films. 13C CP-MAS NMR demonstrates that as added [Na +] increases, partial silk fibroin conformation transit from helix-form to β-form at certain Na + ion concentration which is much higher than that in Bombyx mori silkworm gland. The generalized two-dimensional NMR-NMR correlation analysis reveals that silk fibroin undergoes several intermediate states during its conformation transition process as [Na +] increase. The appearance order of the intermediates is followed as: helix and/or random coil → helix-like → β-sheet-like → β-sheet, which is the same as that produced by pH decrease from 6.8 to 4.8 in the resultant regenerated silk fibroin films. The binding sites of Na + to silk fibroin might involve the carbonyl oxygen atom of certain amino acids sequence which could promote the formation of β-sheet conformation. Since the Na +sbnd O bond is weak, the ability of Na + inducing the secondary structure transition is weaker than those of Ca 2+, Cu 2+ and even K +. It is maybe a reason why the sodium content is much lower than potassium in the silkworm gland.

  12. Multiecho scheme advances surface NMR for aquifer characterization

    NASA Astrophysics Data System (ADS)

    Grunewald, Elliot; Walsh, David

    2013-12-01

    nuclear magnetic resonance (NMR) is increasingly used as a method to noninvasively characterize aquifers. This technology follows a successful history of NMR logging, applied over decades to estimate hydrocarbon reservoir properties. In contrast to logging, however, surface methods have utilized relatively simple acquisition sequences, from which pore-scale properties may not be reliably and efficiently estimated. We demonstrate for the first time the capability of sophisticated multiecho measurements to rapidly record a surface NMR response that more directly reflects aquifer characteristics. Specifically, we develop an adaptation of the multipulse Carr-Purcell-Meiboom-Gill (CPMG) sequence, widely used in logging, to measure the T2 relaxation response in a single scan. We validate this approach in a field surface NMR data set and by direct comparison with an NMR log. Adoption of the CPMG marked a landmark advancement in the history of logging NMR; we have now realized this same advancement in the surface NMR method.

  13. NMR shielding calculations across the periodic table: diamagnetic uranium compounds. 2. Ligand and metal NMR.

    PubMed

    Schreckenbach, Georg

    2002-12-16

    In this and a previous article (J. Phys. Chem. A 2000, 104, 8244), the range of application for relativistic density functional theory (DFT) is extended to the calculation of nuclear magnetic resonance (NMR) shieldings and chemical shifts in diamagnetic actinide compounds. Two relativistic DFT methods are used, ZORA ("zeroth-order regular approximation") and the quasirelativistic (QR) method. In the given second paper, NMR shieldings and chemical shifts are calculated and discussed for a wide range of compounds. The molecules studied comprise uranyl complexes, [UO(2)L(n)](+/-)(q); UF(6); inorganic UF(6) derivatives, UF(6-n)Cl(n), n = 0-6; and organometallic UF(6) derivatives, UF(6-n)(OCH(3))(n), n = 0-5. Uranyl complexes include [UO(2)F(4)](2-), [UO(2)Cl(4)](2-), [UO(2)(OH)(4)](2-), [UO(2)(CO(3))(3)](4-), and [UO(2)(H(2)O)(5)](2+). For the ligand NMR, moderate (e.g., (19)F NMR chemical shifts in UF(6-n)Cl(n)) to excellent agreement [e.g., (19)F chemical shift tensor in UF(6) or (1)H NMR in UF(6-n)(OCH(3))(n)] has been found between theory and experiment. The methods have been used to calculate the experimentally unknown (235)U NMR chemical shifts. A large chemical shift range of at least 21,000 ppm has been predicted for the (235)U nucleus. ZORA spin-orbit appears to be the most accurate method for predicting actinide metal chemical shifts. Trends in the (235)U NMR chemical shifts of UF(6-n)L(n) molecules are analyzed and explained in terms of the calculated electronic structure. It is argued that the energy separation and interaction between occupied and virtual orbitals with f-character are the determining factors. PMID:12470051

  14. NMR studies of nucleic acid dynamics

    PubMed Central

    Al-Hashimi, Hashim M.

    2014-01-01

    Nucleic acid structures have to satisfy two diametrically opposite requirements; on one hand they have to adopt well-defined 3D structures that can be specifically recognized by proteins; on the other hand, their structures must be sufficiently flexible to undergo very large conformational changes that are required during key biochemical processes, including replication, transcription, and translation. How do nucleic acids introduce flexibility into their 3D structure without losing biological specificity? Here, I describe the development and application of NMR spectroscopic techniques in my laboratory for characterizing the dynamic properties of nucleic acids that tightly integrate a broad set of NMR measurements, including residual dipolar couplings, spin relaxation, and relaxation dispersion with sample engineering and computational approaches. This approach allowed us to obtain fundamental new insights into directional flexibility in nucleic acids that enable their structures to change in a very specific functional manner. PMID:24149218

  15. NMR with excitation modulated by Frank sequences.

    PubMed

    Blümich, Bernhard; Gong, Qingxia; Byrne, Eimear; Greferath, Marcus

    2009-07-01

    Miniaturized NMR is of growing importance in bio-, chemical, and -material sciences. Other than the magnet, bulky components are the radio-frequency power amplifier and the power supply or battery pack. We show that constant flip-angle excitation with phase modulation following a particular type of polyphase perfect sequences results in low peak excitation power at high response peak power. It has ideal power distribution in both the time domain and the frequency domain. A savings in peak excitation power of six orders of magnitude has been realized compared to conventionally pulsed excitation. Among others, the excitation promises to be of use for button-cell operated miniature NMR devices as well as for complying with specific-absorption-rate regulations in high-field medical imaging. PMID:19386525

  16. NMR-based diffusion lattice imaging.

    PubMed

    Laun, Frederik Bernd; Müller, Lars; Kuder, Tristan Anselm

    2016-03-01

    Nuclear magnetic resonance (NMR) diffusion experiments are widely employed as they yield information about structures hindering the diffusion process, e.g., about cell membranes. While it has been shown in recent articles that these experiments can be used to determine the shape of closed pores averaged over a volume of interest, it is still an open question how much information can be gained in open well-connected systems. In this theoretical work, it is shown that the full structure information of connected periodic systems is accessible. To this end, the so-called "SEquential Rephasing by Pulsed field-gradient Encoding N Time intervals" (SERPENT) sequence is used, which employs several diffusion encoding gradient pulses with different amplitudes. Two two-dimensional solid matrices that are surrounded by an NMR-visible medium are considered: a hexagonal lattice of cylinders and a rectangular lattice of isosceles triangles. PMID:27078384

  17. Nuclear spin noise in NMR revisited

    SciTech Connect

    Ferrand, Guillaume; Luong, Michel

    2015-09-07

    The theoretical shapes of nuclear spin-noise spectra in NMR are derived by considering a receiver circuit with finite preamplifier input impedance and a transmission line between the preamplifier and the probe. Using this model, it becomes possible to reproduce all observed experimental features: variation of the NMR resonance linewidth as a function of the transmission line phase, nuclear spin-noise signals appearing as a “bump” or as a “dip” superimposed on the average electronic noise level even for a spin system and probe at the same temperature, pure in-phase Lorentzian spin-noise signals exhibiting non-vanishing frequency shifts. Extensive comparisons to experimental measurements validate the model predictions, and define the conditions for obtaining pure in-phase Lorentzian-shape nuclear spin noise with a vanishing frequency shift, in other words, the conditions for simultaneously obtaining the spin-noise and frequency-shift tuning optima.

  18. Multifunctional pulse sequence generator for pulse NMR

    NASA Astrophysics Data System (ADS)

    Wang, Dongsheng

    1988-06-01

    A new multifunctional pulse sequence generator has been designed and constructed. It can conveniently generate various pulse sequences used in nuclear-magnetic resonance (NMR) to measure the spin-lattice relaxation time T1, the spin-spin relaxation time T2, and the spin-locking relaxation time T1 ρ. It can also be used in pulse Fourier transform NMR and double resonance. The intervals of pulses can increase automatically with sequence repetitions and the generator can be used in two-dimensional spectrum measurement and spin-density imaging research. The sequences can be generated through four different triggering methods and there are two synchronous pulse outputs and fifteen auxiliary pulse outputs, so the generator can be conveniently interfaced with a computer or other instruments. The circuitry, functions, and features of the generator are described in this article.

  19. Some nitrogen-14 NMR studies in solids

    SciTech Connect

    Pratum, T.K.

    1983-11-01

    The first order quadrupolar perturbation of the /sup 14/N NMR spectrum yields information regarding the static and dynamic properties of the surrounding electronic environment. Signal to noise problems caused by long /sup 14/N longitudinal relaxation times (T/sub 1/) and small equilibrium polarizations are reduced by rotating frame cross polarization (CP) experiments between /sup 14/N and /sup 1/H. Using quadrupolar echo and CP techniques, the /sup 14/N quadrupolar coupling constants (e/sup 2/qQ/h) and asymmetry parameters (eta) have been obtained for a variety of tetraalkylammonium compounds by observation of their quadrupolar powder patterns at various temperatures. For choline chloride and iodide the /sup 14/N NMR powder patterns exhibit the effects of anisotropic molecular motion, while choline bromide spectra show no such effects.

  20. NMR spectral analysis using prior knowledge

    NASA Astrophysics Data System (ADS)

    Kasai, Takuma; Nagata, Kenji; Okada, Masato; Kigawa, Takanori

    2016-03-01

    Signal assignment is a fundamental step for analyses of protein structure and dynamics with nuclear magnetic resonance (NMR). Main-chain signal assignment is achieved with a sequential assignment method and/or an amino-acid selective stable isotope labeling (AASIL) method. Combinatorial selective labeling (CSL) methods, as well as our labeling strategy, stable isotope encoding (SiCode), were developed to reduce the required number of labeled samples, since one of the drawbacks of AASIL is that many samples are needed. Signal overlapping in NMR spectra interferes with amino-acid determination by CSL and SiCode. Since spectral deconvolution by peak fitting with a gradient method cannot resolve closely overlapped signals, we developed a new method to perform both peak fitting and amino acid determination simultaneously, with a replica exchange Monte Carlo method, incorporating prior knowledge of stable-isotope labeling ratios and the amino-acid sequence of the protein.

  1. NMR-based diffusion lattice imaging

    NASA Astrophysics Data System (ADS)

    Laun, Frederik Bernd; Müller, Lars; Kuder, Tristan Anselm

    2016-03-01

    Nuclear magnetic resonance (NMR) diffusion experiments are widely employed as they yield information about structures hindering the diffusion process, e.g., about cell membranes. While it has been shown in recent articles that these experiments can be used to determine the shape of closed pores averaged over a volume of interest, it is still an open question how much information can be gained in open well-connected systems. In this theoretical work, it is shown that the full structure information of connected periodic systems is accessible. To this end, the so-called "SEquential Rephasing by Pulsed field-gradient Encoding N Time intervals" (SERPENT) sequence is used, which employs several diffusion encoding gradient pulses with different amplitudes. Two two-dimensional solid matrices that are surrounded by an NMR-visible medium are considered: a hexagonal lattice of cylinders and a rectangular lattice of isosceles triangles.

  2. NMR studies of nucleic acid dynamics

    NASA Astrophysics Data System (ADS)

    Al-Hashimi, Hashim M.

    2013-12-01

    Nucleic acid structures have to satisfy two diametrically opposite requirements; on one hand they have to adopt well-defined 3D structures that can be specifically recognized by proteins; on the other hand, their structures must be sufficiently flexible to undergo very large conformational changes that are required during key biochemical processes, including replication, transcription, and translation. How do nucleic acids introduce flexibility into their 3D structure without losing biological specificity? Here, I describe the development and application of NMR spectroscopic techniques in my laboratory for characterizing the dynamic properties of nucleic acids that tightly integrate a broad set of NMR measurements, including residual dipolar couplings, spin relaxation, and relaxation dispersion with sample engineering and computational approaches. This approach allowed us to obtain fundamental new insights into directional flexibility in nucleic acids that enable their structures to change in a very specific functional manner.

  3. Nuclear spin noise in NMR revisited

    NASA Astrophysics Data System (ADS)

    Ferrand, Guillaume; Huber, Gaspard; Luong, Michel; Desvaux, Hervé

    2015-09-01

    The theoretical shapes of nuclear spin-noise spectra in NMR are derived by considering a receiver circuit with finite preamplifier input impedance and a transmission line between the preamplifier and the probe. Using this model, it becomes possible to reproduce all observed experimental features: variation of the NMR resonance linewidth as a function of the transmission line phase, nuclear spin-noise signals appearing as a "bump" or as a "dip" superimposed on the average electronic noise level even for a spin system and probe at the same temperature, pure in-phase Lorentzian spin-noise signals exhibiting non-vanishing frequency shifts. Extensive comparisons to experimental measurements validate the model predictions, and define the conditions for obtaining pure in-phase Lorentzian-shape nuclear spin noise with a vanishing frequency shift, in other words, the conditions for simultaneously obtaining the spin-noise and frequency-shift tuning optima.

  4. Highly flexible pulse programmer for NMR applications

    NASA Technical Reports Server (NTRS)

    Dart, J.; Burum, D. P.; Rhim, W. K.

    1980-01-01

    A pulse generator for NMR application is described. Eighteen output channels are provided to allow use in single and double resonance experiments. Complex pulse sequences may be generated by loading instructions into a 256-word by 16-bit program memory. Features of the pulse generator include programmable time delays from 0.5 micros to 1000 s, branching and looping instructions, and the ability to be loaded and operated either manually or from a PDP-11/10 computer.

  5. Quantitative calibration of radiofrequency NMR Stark effects

    NASA Astrophysics Data System (ADS)

    Tarasek, Matthew R.; Kempf, James G.

    2011-10-01

    Nuclear magnetic resonance (NMR) Stark responses can occur in quadrupolar nuclei for an electric field oscillating at twice the usual NMR frequency (2ω0). Calibration of responses to an applied E field is needed to establish nuclear spins as probes of native E fields within material and molecular systems. We present an improved approach and apparatus for accurate measurement of quadrupolar Stark effects. Updated values of C14 (the response parameter in cubic crystals) were obtained for both 69Ga and 75As in GaAs. Keys to improvement include a modified implementation of voltage dividers to assess the 2ω0 amplitude, |E|, and the stabilization of divider response by reduction of stray couplings in 2ω0 circuitry. Finally, accuracy was enhanced by filtering sets of |E| through a linear response function that we established for the radiofrequency amplifier. Our approach is verified by two types of spectral results. Steady-state 2ω0 excitation to presaturate NMR spectra yielded C14 = (2.59 ± 0.06) × 1012 m-1 for 69Ga at room-temperature and 14.1 T. For 75As, we obtained (3.1 ± 0.1) × 1012 m-1. Both values reconcile with earlier results from 77 K and below 1 T, whereas current experiments are at room temperature and 14.1 T. Finally, we present results where few-microsecond pulses of the 2ω0 field induced small (tens of Hz) changes in high-resolution NMR line shapes. There too, spectra collected vs |E| agree with the model for response, further establishing the validity of our protocols to specify |E|.

  6. Theory of NMR in Superconducting Multilayers

    NASA Astrophysics Data System (ADS)

    Kuboki, Kazuhiro; Fukuyama, Hidetoshi

    1988-09-01

    Motivated by experiments of NMR on superconductor(S)-normal-metal(N) multi-layer system, we have calculated the nuclear spin-lattice relaxation rate, T1-1, for both N and S layers based on the bilayer model of McMillan for the proximity effect. The results of calculation are in essential agreement with experiments by Aoki et al. and Imai et al.

  7. Theory of NMR for superconducting superlattices

    NASA Astrophysics Data System (ADS)

    Kuboki, Kazuhiro; Fukuyama, Hidetoshi

    1988-06-01

    Motivated by experiments of NMR on superconductor(S)-normal-metal(N) multilayer system, we have calculated the nuclear spin-lattice relaxation rate,T1-1, for both N and S metals based on the bilayer model of McMillan for the proximity effect. The results of calculations are in essential agreement with experiments by Aoki et al. and Imai et al.

  8. Multiple-quantum NMR in solids

    NASA Astrophysics Data System (ADS)

    Yen, Yu-Sze; Pines, A.

    1983-03-01

    Multiple-quantum NMR has typically been observed in small groups of spins in isolated molecules. Due to the profusion of spin transitions in a solid, individual lines are unresolved. Excitation of high quantum transitions by normal schemes is thus difficult. To ensure that overlapping lines add constructively and to enhance sensitivity, time-reversal pulse sequences are used to generate all lines in phase. Up to 22-quantum 1H absorption in solid adamantane is observed.

  9. Multiple-quantum NMR in solids

    SciTech Connect

    Yen, Y.; Pines, A.

    1983-03-15

    Multiple-quantum NMR has typically been observed in small groups of spins in isolated molecules. Due to the profusion of spin transitions in a solid, individual lines are unresolved. Excitation of high quantum transitions by normal schemes is thus difficult. To ensure that overlapping lines add constructively and to enhance sensitivity, time-reversal pulse sequences are used to generate all lines in phase. Up to 22-quantum /sup 1/H absorption in solid adamantane is observed.

  10. Nonclassical correlation in NMR quadrupolar systems

    SciTech Connect

    Soares-Pinto, D. O.; Auccaise, R.; Azevedo, E. R. de; Bonagamba, T. J.; Celeri, L. C.; Maziero, J.; Serra, R. M.; Fanchini, F. F.

    2010-06-15

    The existence of quantum correlation (as revealed by quantum discord), other than entanglement and its role in quantum-information processing (QIP), is a current subject for discussion. In particular, it has been suggested that this nonclassical correlation may provide computational speedup for some quantum algorithms. In this regard, bulk nuclear magnetic resonance (NMR) has been successfully used as a test bench for many QIP implementations, although it has also been continuously criticized for not presenting entanglement in most of the systems used so far. In this paper, we report a theoretical and experimental study on the dynamics of quantum and classical correlations in an NMR quadrupolar system. We present a method for computing the correlations from experimental NMR deviation-density matrices and show that, given the action of the nuclear-spin environment, the relaxation produces a monotonic time decay in the correlations. Although the experimental realizations were performed in a specific quadrupolar system, the main results presented here can be applied to whichever system uses a deviation-density matrix formalism.

  11. Statistical filtering for NMR based structure generation

    PubMed Central

    2011-01-01

    The constitutional assignment of natural products by NMR spectroscopy is usually based on 2D NMR experiments like COSY, HSQC, and HMBC. The difficulty of a structure elucidation problem depends more on the type of the investigated molecule than on its size. Saturated compounds can usually be assigned unambiguously by hand using only COSY and 13C-HMBC data, whereas condensed heterocycles are problematic due to their lack of protons that could show interatomic connectivities. Different computer programs were developed to aid in the structural assignment process, one of them COCON. In the case of unsaturated and substituted molecules structure generators frequently will generate a very large number of possible solutions. This article presents a "statistical filter" for the reduction of the number of results. The filter works by generating 3D conformations using smi23d, a simple MD approach. All molecules for which the generation of constitutional restraints failed were eliminated from the result set. Some structural elements removed by the statistical filter were analyzed and checked against Beilstein. The automatic removal of molecules for which no MD parameter set could be created was included into WEBCOCON. The effect of this filter varies in dependence of the NMR data set used, but in no case the correct constitution was removed from the resulting set. PMID:21835037

  12. NMR methodologies for studying mitochondrial bioenergetics.

    PubMed

    Alves, Tiago C; Jarak, Ivana; Carvalho, Rui A

    2012-01-01

    Nuclear magnetic resonance (NMR) spectroscopy is a technique with an increasing importance in the study of metabolic diseases. Its initial important role in the determination of chemical structures (1, 2) has been considerably overcome by its potential for the in vivo study of metabolism (3-5). The main characteristic that makes this technique so attractive is its noninvasiveness. Only nuclei capable of transitioning between energy states, in the presence of an intense and constant magnetic field, are studied. This includes abundant nuclei such as proton ((1)H) and phosphorous ((31)P), as well as stable isotopes such as deuterium ((2)H) and carbon 13 ((13)C). This allows a wide range of applications that vary from the determination of water distribution in tissues (as obtained in a magnetic resonance imaging scan) to the calculation of metabolic fluxes under ex vivo and in vivo conditions without the need to use radioactive tracers or tissue biopsies (as in a magnetic resonance spectroscopy (MRS) scan). In this chapter, some technical aspects of the methodology of an NMR/MRS experiment as well as how it can be used to study mitochondrial bioenergetics are overviewed. Advantages and disadvantages of in vivo MRS versus high-resolution NMR using proton high rotation magic angle spinning (HRMAS) of tissue biopsies and tissue extracts are also discussed. PMID:22057574

  13. Sol-gel kinetics by NMR

    SciTech Connect

    Assink, R.A.; Kay, B.D.

    1991-01-01

    The chemical synthesis of advanced ceramic and glass materials by the sol-gel process has become an area of increasing activity in the field of material science. The sol-gel process provides a means to prepare homogeneous, high purity materials with tailored chemical and physical properties. This paper surveyed the nuclear magnetic resonance (NMR) studies of silicon-based sol-gel kinetics. A review of the various models which have been used to analyze the chemical kinetics of various sol-gel systems was presented. The utility of NMR spectroscopy was demonstrated in investigating the influence that various reaction conditions have on the reaction pathways by which sol-gel derived materials are synthesized. By observing in a direct fashion the chemical pathway of the sol-gel, it is often possible to relate the final properties of the material to the formulation and reaction conditions of the sol-gel. The study of reaction kinetics by NMR is expected to play an increasingly important role in understanding sol-gel processing and material properties. 15 refs. (DP)

  14. DFT and NMR parameterized conformation of valeranone.

    PubMed

    Torres-Valencia, J Martín; Meléndez-Rodríguez, Myriam; Alvarez-García, Rocío; Cerda-García-Rojas, Carlos M; Joseph-Nathan, Pedro

    2004-10-01

    A Monte Carlo random search using molecular mechanics, followed by geometry optimization of each minimum energy structure employing density functional theory (DFT) calculations at the B3LYP/6-31G* level and a Boltzmann analysis of the total energies, generated accurate molecular models which describe the conformational behavior of the antispasmodic bicyclic sesquiterpene valeranone (1). The theoretical H-C-C-H dihedral angles gave the corresponding 1H, 1H vicinal coupling constants using a generalized Karplus-type equation. In turn, the 3J(H,H) values were used as initial input data for the spectral simulation of 1, which after iteration provided an excellent correlation with the experimental 1H NMR spectrum. The calculated 3J(H,H) values closely predicted the experimental values, excepting the coupling constant between the axial hydrogen alpha to the carbonyl group and the equatorial hydrogen beta to the carbonyl group (J(2beta, 3beta)). The difference is explained in terms of the electron density distribution found in the highest occupied molecular orbital (HOMO) of 1. The simulated spectrum, together with 2D NMR experiments, allowed the total assignment of the 1H and 13C NMR spectra of 1. PMID:15366065

  15. Rhodopsin-lipid interactions studied by NMR.

    PubMed

    Soubias, Olivier; Gawrisch, Klaus

    2013-01-01

    The biophysical properties of the lipid matrix are known to influence function of integral membrane proteins. We report on a sample preparation method for reconstitution of membrane proteins which uses porous anodic aluminum oxide (AAO) filters with 200-nm-wide pores of high density. The substrate permits formation of tubular, single membranes that line the inner surface of pores. One square centimeter of filter with a thickness of 60μm yields on the order of 500cm(2) of solid-supported single bilayer surface, sufficient for NMR studies. The tubular bilayers are free of detergent, fully hydrated, and accessible for ligands from one side of the membrane. The use of AAO filters greatly improves reproducibility of the reconstitution process such that the influence of protein on lipid order parameters can be studied with high resolution. As an example, results for the G protein-coupled receptor of class A, bovine rhodopsin, are shown. By (2)H NMR order parameter measurements, it is detected that rhodopsin insertion elastically deforms membranes near the protein. Furthermore, by (1)H saturation-transfer NMR under conditions of magic angle spinning, we demonstrate detection of preferences in interactions of rhodopsin with particular lipid species. It is assumed that function of integral membrane proteins depends on both protein-induced elastic deformations of the lipid matrix and preferences for interaction of the protein with particular lipid species in the first layer of lipids surrounding the protein. PMID:23374188

  16. NMR quantitation: influence of RF inhomogeneity

    PubMed Central

    Mo, Huaping; Harwood, John; Raftery, Daniel

    2016-01-01

    The NMR peak integral is ideally linearly dependent on the sine of excitation angle (θ), which has provided unsurpassed flexibility in quantitative NMR by allowing the use of a signal of any concentration as the internal concentration reference. Controlling the excitation angle is particularly critical for solvent proton concentration referencing to minimize the negative impact of radiation damping, and to reduce the risk of receiver gain compression. In practice, due to the influence of RF inhomogeneity for any given probe, the observed peak integral is not exactly proportional to sin θ. To evaluate the impact quantitatively, we introduce a RF inhomogeneity factor I(θ) as a function of the nominal pulse excitation angle and propose a simple calibration procedure. Alternatively, I(θ) can be calculated from the probe’s RF profile, which can be readily obtained as a gradient image of an aqueous sample. Our results show that without consideration of I(θ), even for a probe with good RF homogeneity, up to 5% error can be introduced due to different excitation pulse angles used for the analyte and the reference. Hence, a simple calibration of I(θ) can eliminate such errors and allow an accurate description of the observed NMR signal’s dependence on the excitation angle in quantitative analysis. PMID:21919056

  17. Earth's field NMR; a surface moisture detector?

    NASA Astrophysics Data System (ADS)

    Fukushima, Eiichi; Altobelli, Stephen; McDowell, Andrew; Zhang, Tongsheng

    2012-10-01

    Earth's field NMR (EFNMR), being free of magnets, would be an ideal teaching medium as well as a mobile NMR technique except for its weak S/N. The common EFNMR apparatus uses a powerful prepolarization field to enhance the spin magnetization before the experiment. We introduce a coil design geared to larger but manageable samples with sufficient sensitivity without prepolarization to move EFNMR closer to routine use and to provide an inexpensive teaching tool. Our coil consists of parallel wires spread out on a plywood to form a current sheet with the current return wires separated so they will not influence the main part of the coil assembly. The sensitive region is a relatively thin region parallel to the coil and close to it. A single turn of the coil is wound to be topologically equivalent to a figure-8. The two crossing segments in the center of a figure-8 form two of the parallel wires of the flat coil. Thus, a two-turn figure-8 has four crossing wires so its topologically equivalent coil will have four parallel wires with currents in phase. Together with the excellent sensitivity, this coil offers outstanding interference rejection because of the figure-8 geometry. An example of such a coil has 328 parallel wires covering a ˜1 meter square plywood which yields a good NMR signal from 26 liters of water spread out roughly over the area of the coil in less than one minute in a nearby park.

  18. NMR Studies of Dynamic Biomolecular Conformational Ensembles

    PubMed Central

    Torchia, Dennis A.

    2015-01-01

    Multidimensional heteronuclear NMR approaches can provide nearly complete sequential signal assignments of isotopically enriched biomolecules. The availability of assignments together with measurements of spin relaxation rates, residual spin interactions, J-couplings and chemical shifts provides information at atomic resolution about internal dynamics on timescales ranging from ps to ms, both in solution and in the solid state. However, due to the complexity of biomolecules, it is not possible to extract a unique atomic-resolution description of biomolecular motions even from extensive NMR data when many conformations are sampled on multiple timescales. For this reason, powerful computational approaches are increasingly applied to large NMR data sets to elucidate conformational ensembles sampled by biomolecules. In the past decade, considerable attention has been directed at an important class of biomolecules that function by binding to a wide variety of target molecules. Questions of current interest are: “Does the free biomolecule sample a conformational ensemble that encompasses the conformations found when it binds to various targets; and if so, on what time scale is the ensemble sampled?” This article reviews recent efforts to answer these questions, with a focus on comparing ensembles obtained for the same biomolecules by different investigators. A detailed comparison of results obtained is provided for three biomolecules: ubiquitin, calmodulin and the HIV-1 trans-activation response RNA. PMID:25669739

  19. Discrete analysis of stochastic NMR.II

    NASA Astrophysics Data System (ADS)

    Wong, S. T. S.; Rods, M. S.; Newmark, R. D.; Budinger, T. F.

    Stochastic NMR is an efficient technique for high-field in vivo imaging and spectroscopic studies where the peak RF power required may be prohibitively high for conventional pulsed NMR techniques. A stochastic NMR experiment excites the spin system with a sequence of RF pulses where the flip angles or the phases of the pulses are samples of a discrete stochastic process. In a previous paper the stochastic experiment was analyzed and analytic expressions for the input-output cross-correlations, average signal power, and signal spectral density were obtained for a general stochastic RF excitation. In this paper specific cases of excitation with random phase, fixed flip angle, and excitation with two random components in quadrature are analyzed. The input-output cross-correlation for these two types of excitations is shown to be Lorentzian. Line broadening is the only spectral distortion as the RF excitation power is increased. The systematic noise power is inversely proportional to the number of data points N used in the spectral reconstruction. The use of a complete maximum length sequence (MLS) may improve the signal-to-systematic-noise ratio by 20 dB relative to random binary excitation, but peculiar features in the higher-order autocorrelations of MLS cause noise-like distortion in the reconstructed spectra when the excitation power is high. The amount of noise-like distortion depends on the choice of the MLS generator.

  20. Calibration of NMR well logs from carbonate reservoirs with laboratory NMR measurements and μXRCT

    DOE PAGESBeta

    Mason, Harris E.; Smith, Megan M.; Hao, Yue; Carroll, Susan A.

    2014-12-31

    The use of nuclear magnetic resonance (NMR) well log data has the potential to provide in-situ porosity, pore size distributions, and permeability of target carbonate CO₂ storage reservoirs. However, these methods which have been successfully applied to sandstones have yet to be completely validated for carbonate reservoirs. Here, we have taken an approach to validate NMR measurements of carbonate rock cores with independent measurements of permeability and pore surface area to volume (S/V) distributions using differential pressure measurements and micro X-ray computed tomography (μXRCT) imaging methods, respectively. We observe that using standard methods for determining permeability from NMR data incorrectlymore » predicts these values by orders of magnitude. However, we do observe promise that NMR measurements provide reasonable estimates of pore S/V distributions, and with further independent measurements of the carbonate rock properties that universally applicable relationships between NMR measured properties may be developed for in-situ well logging applications of carbonate reservoirs.« less

  1. Guiding automated NMR structure determination using a global optimization metric, the NMR DP score.

    PubMed

    Huang, Yuanpeng Janet; Mao, Binchen; Xu, Fei; Montelione, Gaetano T

    2015-08-01

    ASDP is an automated NMR NOE assignment program. It uses a distinct bottom-up topology-constrained network anchoring approach for NOE interpretation, with 2D, 3D and/or 4D NOESY peak lists and resonance assignments as input, and generates unambiguous NOE constraints for iterative structure calculations. ASDP is designed to function interactively with various structure determination programs that use distance restraints to generate molecular models. In the CASD-NMR project, ASDP was tested and further developed using blinded NMR data, including resonance assignments, either raw or manually-curated (refined) NOESY peak list data, and in some cases (15)N-(1)H residual dipolar coupling data. In these blinded tests, in which the reference structure was not available until after structures were generated, the fully-automated ASDP program performed very well on all targets using both the raw and refined NOESY peak list data. Improvements of ASDP relative to its predecessor program for automated NOESY peak assignments, AutoStructure, were driven by challenges provided by these CASD-NMR data. These algorithmic improvements include (1) using a global metric of structural accuracy, the discriminating power score, for guiding model selection during the iterative NOE interpretation process, and (2) identifying incorrect NOESY cross peak assignments caused by errors in the NMR resonance assignment list. These improvements provide a more robust automated NOESY analysis program, ASDP, with the unique capability of being utilized with alternative structure generation and refinement programs including CYANA, CNS, and/or Rosetta. PMID:26081575

  2. Development of Halbach magnet for portable NMR device

    NASA Astrophysics Data System (ADS)

    Doğan, N.; Topkaya, R.; Subaşi, H.; Yerli, Y.; Rameev, B.

    2009-03-01

    Nuclear magnetic resonance (NMR) has enormous potential for various applications in industry as the on-line or at-line test/control device of process environments. Advantage of NMR is its non-destructive nature, because it does not require the measurement probe to have a contact with the tested media. Despite of the recent progress in this direction, application of NMR in industry is still very limited. This is related to the technical and analytical complications of NMR as a method, and high cost of NMR analyzers available at the market. However in many applications, NMR is a very useful technique to test various products and to monitor quantitatively industrial processes. Fortunately usually there is no need in a high-field superconducting magnets to obtain the high-resolution spectra with the detailed information on chemical shifts and coupling-constant. NMR analyzers are designed to obtain the relaxation parameters by measuring the NMR spectra in the time domain rather than in frequency domain. Therefore it is possible to use small magnetic field (and low frequency of 2-60 MHz) in NMR systems, based on permanent magnet technology, which are specially designed for specific at-line and on-line process applications. In this work we present the permanent magnet system developed to use in the portative NMR devices. We discuss the experimental parameters of the designed Halbach magnet system and compare them with results of theoretical modelling.

  3. Protein Structure Determination Using Protein Threading and Sparse NMR Data

    SciTech Connect

    Crawford, O.H.; Einstein, J.R.; Xu, D.; Xu, Y.

    1999-11-14

    It is well known that the NMR method for protein structure determination applies to small proteins and that its effectiveness decreases very rapidly as the molecular weight increases beyond about 30 kD. We have recently developed a method for protein structure determination that can fully utilize partial NMR data as calculation constraints. The core of the method is a threading algorithm that guarantees to find a globally optimal alignment between a query sequence and a template structure, under distance constraints specified by NMR/NOE data. Our preliminary tests have demonstrated that a small number of NMR/NOE distance restraints can significantly improve threading performance in both fold recognition and threading-alignment accuracy, and can possibly extend threading's scope of applicability from structural homologs to structural analogs. An accurate backbone structure generated by NMR-constrained threading can then provide a significant amount of structural information, equivalent to that provided by the NMR method with many NMR/NOE restraints; and hence can greatly reduce the amount of NMR data typically required for accurate structure determination. Our preliminary study suggests that a small number of NMR/NOE restraints may suffice to determine adequately the all-atom structure when those restraints are incorporated in a procedure combining threading, modeling of loops and sidechains, and molecular dynamics simulation. Potentially, this new technique can expand NMR's capability to larger proteins.

  4. NMR spectroscopy of experimentally shocked single crystal quartz: A reexamination of the NMR shock barometer

    NASA Technical Reports Server (NTRS)

    Fiske, P. S.; Gratz, A. J.; Nellis, W. J.

    1993-01-01

    Cygan and others report a broadening of the Si-29 nuclear magnetic resonance (NMR) peak for synthetic quartz powders with increasing shock pressure which they propose as a shock wave barometer for natural systems. These results are expanded by studying single crystal quartz shocked to 12 and 33 GPa using the 6.5 m two-stage light-gas gun at Lawrence Livermore National Laboratories. Our NMR results differ substantially from those of Cygan and others and suggest that the proposed shock wave barometer may require refinement. The difference in results between this study and that of Cygan and others is most likely caused by different starting materials (single crystal vs. powder) and different shock loading histories. NMR results from single crystal studies may be more applicable to natural systems.

  5. A Reinvestigation of Ramsey's Theory of NMR Coupling

    NASA Astrophysics Data System (ADS)

    Ajith Perera, S.; Bartlett, Rodney J.

    A systematic development of relativistic molecular Hamiltonians and various non-relativistic approximations are presented. Our starting point is the Dirac one-fermion Hamiltonian in the presence of an external electromagnetic field. The problems associated with generalizing [`]Dirac's one-fermion theory' smoothly to more than one fermion are discussed. The description of many-fermion systems within the framework of quantum electrodynamics (QED) will lead to Hamiltonians which do not suffer from the problems associated with the direct extension of [`]Dirac's one-fermion theory' to many-fermion system. An exhaustive discussion of the recent QED developments in the relevant area is not presented, except for cursory remarks for completeness. The non-relativistic form (NRF) of the many-electron relativistic Hamiltonian is developed as the working Hamiltonian. It is used to extract operators for the observables, which represent the response of a molecule to an external electromagnetic radiation field. In this study, our focus is mainly on the operators which eventually were used to calculate the nuclear magnetic resonance (NMR) chemical shifts and indirect nuclear spin-spin coupling constants.

  6. Fast automated protein NMR data collection and assignment by ADAPT-NMR on Bruker spectrometers

    NASA Astrophysics Data System (ADS)

    Lee, Woonghee; Hu, Kaifeng; Tonelli, Marco; Bahrami, Arash; Neuhardt, Elizabeth; Glass, Karen C.; Markley, John L.

    2013-11-01

    ADAPT-NMR (Assignment-directed Data collection Algorithm utilizing a Probabilistic Toolkit in NMR) supports automated NMR data collection and backbone and side chain assignment for [U-13C, U-15N]-labeled proteins. Given the sequence of the protein and data for the orthogonal 2D 1H-15N and 1H-13C planes, the algorithm automatically directs the collection of tilted plane data from a variety of triple-resonance experiments so as to follow an efficient pathway toward the probabilistic assignment of 1H, 13C, and 15N signals to specific atoms in the covalent structure of the protein. Data collection and assignment calculations continue until the addition of new data no longer improves the assignment score. ADAPT-NMR was first implemented on Varian (Agilent) spectrometers [A. Bahrami, M. Tonelli, S.C. Sahu, K.K. Singarapu, H.R. Eghbalnia, J.L. Markley, PLoS One 7 (2012) e33173]. Because of broader interest in the approach, we present here a version of ADAPT-NMR for Bruker spectrometers. We have developed two AU console programs (ADAPT_ORTHO_run and ADAPT_NMR_run) that run under TOPSPIN Versions 3.0 and higher. To illustrate the performance of the algorithm on a Bruker spectrometer, we tested one protein, chlorella ubiquitin (76 amino acid residues), that had been used with the Varian version: the Bruker and Varian versions achieved the same level of assignment completeness (98% in 20 h). As a more rigorous evaluation of the Bruker version, we tested a larger protein, BRPF1 bromodomain (114 amino acid residues), which yielded an automated assignment completeness of 86% in 55 h. Both experiments were carried out on a 500 MHz Bruker AVANCE III spectrometer equipped with a z-gradient 5 mm TCI probe. ADAPT-NMR is available at http://pine.nmrfam.wisc.edu/ADAPT-NMR in the form of pulse programs, the two AU programs, and instructions for installation and use.

  7. Fast automated protein NMR data collection and assignment by ADAPT-NMR on Bruker spectrometers.

    PubMed

    Lee, Woonghee; Hu, Kaifeng; Tonelli, Marco; Bahrami, Arash; Neuhardt, Elizabeth; Glass, Karen C; Markley, John L

    2013-11-01

    ADAPT-NMR (Assignment-directed Data collection Algorithm utilizing a Probabilistic Toolkit in NMR) supports automated NMR data collection and backbone and side chain assignment for [U-(13)C, U-(15)N]-labeled proteins. Given the sequence of the protein and data for the orthogonal 2D (1)H-(15)N and (1)H-(13)C planes, the algorithm automatically directs the collection of tilted plane data from a variety of triple-resonance experiments so as to follow an efficient pathway toward the probabilistic assignment of (1)H, (13)C, and (15)N signals to specific atoms in the covalent structure of the protein. Data collection and assignment calculations continue until the addition of new data no longer improves the assignment score. ADAPT-NMR was first implemented on Varian (Agilent) spectrometers [A. Bahrami, M. Tonelli, S.C. Sahu, K.K. Singarapu, H.R. Eghbalnia, J.L. Markley, PLoS One 7 (2012) e33173]. Because of broader interest in the approach, we present here a version of ADAPT-NMR for Bruker spectrometers. We have developed two AU console programs (ADAPT_ORTHO_run and ADAPT_NMR_run) that run under TOPSPIN Versions 3.0 and higher. To illustrate the performance of the algorithm on a Bruker spectrometer, we tested one protein, chlorella ubiquitin (76 amino acid residues), that had been used with the Varian version: the Bruker and Varian versions achieved the same level of assignment completeness (98% in 20 h). As a more rigorous evaluation of the Bruker version, we tested a larger protein, BRPF1 bromodomain (114 amino acid residues), which yielded an automated assignment completeness of 86% in 55 h. Both experiments were carried out on a 500 MHz Bruker AVANCE III spectrometer equipped with a z-gradient 5 mm TCI probe. ADAPT-NMR is available at http://pine.nmrfam.wisc.edu/ADAPT-NMR in the form of pulse programs, the two AU programs, and instructions for installation and use. PMID:24091140

  8. NMR Wool Tube: a novel method for NMR solution analysis of derivatized glass surfaces.

    PubMed

    Cholewa, Olivia Maria

    2004-08-13

    Glass wool was placed within an NMR tube as a solid support for the covalent attachment of a molecule to allow for a simple one-dimensional 1H FT NMR solution analysis. This novel procedure avoids the use of expensive sample tubes or platforms, as required for magic angle or fast spinning, exotic pulse sequences, isotopic labeling or the use of a large number of scans to provide the ability to analyze the structure, mobility, ligand binding, and solvent interactions of the surface bound molecule. PMID:15387199

  9. Oil droplet size determination in complex flavor delivery systems by diffusion NMR spectroscopy.

    PubMed

    Fieber, Wolfgang; Hafner, Valeria; Normand, Valéry

    2011-04-15

    Droplet size distribution of flavor oils in two different solid flavor delivery systems were determined with pulsed field gradient NMR spectroscopy: yeast encapsulation system, a spray dried flavor encapsulation system based on empty yeast cells, and glassy encapsulation system, an extruded solid water soluble carbohydrate delivery system. The oil droplet sizes are limited by the yeast cell walls in the yeast encapsulation system and the size distribution is unimodal according to images from transmission electron microscopy. The droplet size determination with diffusion NMR is based on the Murday and Cotts theory of restricted diffusion of liquids in geometrical confinements. Good fits of the diffusion data could be obtained by applying a unimodal, log-normal size distribution model and average droplet sizes of about 2 μm were found that correspond approximately to the inner diameter of the yeast cells. Scanning electron microscopy images showed a multimodal droplet size distribution in the glassy extruded delivery systems. To fit the NMR data a bimodal log-normal distribution function with five independent fitting parameters was implemented that yielded consistent and robust results. The two size populations were found in the micron and sub-micron range, respectively. The method was sufficiently accurate to depict variation of droplet size distributions in glassy encapsulation systems of different formulation. PMID:21316700

  10. Isotope labeling for NMR studies of macromolecular structure and interactions

    SciTech Connect

    Wright, P.E.

    1994-12-01

    Implementation of biosynthetic methods for uniform or specific isotope labeling of proteins, coupled with the recent development of powerful heteronuclear multidimensional NMR methods, has led to a dramatic increase in the size and complexity of macromolecular systems that are now amenable to NMR structural analysis. In recent years, a new technology has emerged that combines uniform {sup 13}C, {sup 15}N labeling with heteronuclear multidimensional NMR methods to allow NMR structural studies of systems approaching 25 to 30 kDa in molecular weight. In addition, with the introduction of specific {sup 13}C and {sup 15}N labels into ligands, meaningful NMR studies of complexes of even higher molecular weight have become feasible. These advances usher in a new era in which the earlier, rather stringent molecular weight limitations have been greatly surpassed and NMR can begin to address many central biological problems that involve macromolecular structure, dynamics, and interactions.

  11. Fluid-Rock Characterization and Interactions in NMR Well Logging

    SciTech Connect

    Hirasaki, George J.; Mohanty, Kishore K.

    2003-02-10

    The objective of this project was to characterize the fluid properties and fluid-rock interactions that are needed for formation evaluation by NMR well logging. The advances made in the understanding of NMR fluid properties are summarized in a chapter written for an AAPG book on NMR well logging. This includes live oils, viscous oils, natural gas mixtures, and the relation between relaxation time and diffusivity.

  12. Magic-angle-spinning NMR studies of zeolite SAPO-5

    NASA Astrophysics Data System (ADS)

    Freude, D.; Ernst, H.; Hunger, M.; Pfeifer, H.; Jahn, E.

    1988-01-01

    SAPO-5 was synthesized using triethylamine as template. Magic-angle-spinning (MAS) NMR of 1H, 27Al, 29Si and 31P was used to study the silicon incorporation into the framework and the nature of the Brønsted sites. 1H MAS NMR shows two types of bridging hydroxyl groups. 29Si MAS NMR indicates that silicon substitutes mostly for phosphorus and that there is a small amount of crystalline SiO 2 in the zeolite powder.

  13. Lithium Polymer Electrolytes and Solid State NMR

    NASA Technical Reports Server (NTRS)

    Berkeley, Emily R.

    2004-01-01

    Research is being done at the Glenn Research Center (GRC) developing new kinds of batteries that do not depend on a solution. Currently, batteries use liquid electrolytes containing lithium. Problems with the liquid electrolyte are (1) solvents used can leak out of the battery, so larger, more restrictive, packages have to be made, inhibiting the diversity of application and decreasing the power density; (2) the liquid is incompatible with the lithium metal anode, so alternative, less efficient, anodes are required. The Materials Department at GRC has been working to synthesize polymer electrolytes that can replace the liquid electrolytes. The advantages are that polymer electrolytes do not have the potential to leak so they can be used for a variety of tasks, small or large, including in the space rover or in space suits. The polymers generated by Dr. Mary Ann Meador's group are in the form of rod -coil structures. The rod aspect gives the polymer structural integrity, while the coil makes it flexible. Lithium ions are used in these polymers because of their high mobility. The coils have repeating units of oxygen which stabilize the positive lithium by donating electron density. This aids in the movement of the lithium within the polymer, which contributes to higher conductivity. In addition to conductivity testing, these polymers are characterized using DSC, TGA, FTIR, and solid state NMR. Solid state NMR is used in classifying materials that are not soluble in solvents, such as polymers. The NMR spins the sample at a magic angle (54.7') allowing the significant peaks to emerge. Although solid state NMR is a helpful technique in determining bonding, the process of preparing the sample and tuning it properly are intricate jobs that require patience; especially since each run takes about six hours. The NMR allows for the advancement of polymer synthesis by showing if the expected results were achieved. Using the NMR, in addition to looking at polymers, allows for

  14. Understanding NMR relaxometry of partially water-saturated rocks

    NASA Astrophysics Data System (ADS)

    Mohnke, O.; Jorand, R.; Nordlund, C.; Klitzsch, N.

    2015-06-01

    Nuclear magnetic resonance (NMR) relaxometry measurements are commonly used to characterize the storage and transport properties of water-saturated rocks. Estimations of these properties are based on the direct link of the initial NMR signal amplitude to porosity (water content) and of the NMR relaxation time to pore size. Herein, pore shapes are usually assumed to be spherical or cylindrical. However, the NMR response at partial water saturation for natural sediments and rocks may differ strongly from the responses calculated for spherical or cylindrical pores, because these pore shapes do not account for water menisci remaining in the corners of desaturated angular pores. Therefore, we consider a bundle of pores with triangular cross sections. We introduce analytical solutions of the NMR equations at partial saturation of these pores, which account for water menisci of desaturated pores. After developing equations that describe the water distribution inside the pores, we calculate the NMR response at partial saturation for imbibition and drainage based on the deduced water distributions. For this pore model, the NMR amplitudes and NMR relaxation times at partial water saturation strongly depend on pore shape, i.e., arising from the capillary pressure and pore shape-dependent water distribution in desaturated pores with triangular cross sections. Even so, the NMR relaxation time at full saturation only depends on the surface-to-volume ratio of the pore. Moreover, we show the qualitative agreement of the saturation-dependent relaxation-time distributions of our model with those observed for rocks and soils.

  15. Rotational Doppler Effect and Barnett Field in Spinning NMR

    NASA Astrophysics Data System (ADS)

    Chudo, Hiroyuki; Harii, Kazuya; Matsuo, Mamoru; Ieda, Jun'ichi; Ono, Masao; Maekawa, Sadamichi; Saitoh, Eiji

    2015-04-01

    We report the observation of the rotational Doppler effect using nuclear magnetic resonance (NMR). We have developed a coil-spinning technique that enables measurements by rotating a detector and fixing a sample. We found that the rotational Doppler effect gives rise to NMR frequency shifts equal to the rotation frequency. We formulate the rotational Doppler effect and the Barnett field using a vector model for the nuclear magnetic moment. This formulation reveals that, with just the sample rotating, both effects cancel each other, thereby explaining the absence of an NMR frequency shift in conventional sample-spinning NMR measurements.

  16. Measurement of vorticity diffusion by NMR microscopy.

    PubMed

    Brown, Jennifer R; Callaghan, Paul T

    2010-05-01

    In a Newtonian fluid, vorticity diffuses at a rate determined by the kinematic viscosity. Here we use rapid NMR velocimetry, based on a RARE sequence, to image the time-dependent velocity field on startup of a fluid-filled cylinder and therefore measure the diffusion of vorticity. The results are consistent with the solution to the vorticity diffusion equation where the angular velocity on the outside surface of the fluid, at the cylinder's rotating wall, is fixed. This method is a means of measuring kinematic viscosity for low viscosity fluids without the need to measure stress. PMID:20189854

  17. Analysis of multiple pulse NMR in solids

    NASA Technical Reports Server (NTRS)

    Rhim, W.-K.; Elleman, D. D.; Vaughan, R. W.

    1973-01-01

    The general problems associated with the removal of the effects of dipolar broadening from solid-state NMR spectra are analyzed. The effects of finite pulse width and H sub 1 inhomogeneity are shown to have limited the resolution of previous pulse cycles, and a new eight-pulse cycle designed to minimize these problems is discussed. Spectra for F-19 in CaF2 taken with this cycle are presented which show residual linewidth near 10 Hz. The feasibility of measuring proton chemical shift tensors is discussed.

  18. NMR Characterizations of Properties of Heterogeneous Media

    SciTech Connect

    Uh, Jinsoo; Phan, Jack; Xue, Dong; Watson, A. Ted

    2003-01-28

    The overall goal of this project was to develop reliable methods for resolving macroscopic properties important for describing the flow of one or more fluid phases in reservoirs from formation measurements. During this reporting period, the determination of surface relaxivity from NMR data was investigated. A new method for determining the surface relaxivity from measured data was developed and tested with data obtained from an Exxon sample. The new method avoids the use of a certain mathematical short-time approximation in the data analysis, which has been shown to be unsuitable.

  19. NMR measurements in SSC dipole D00001

    SciTech Connect

    Kuchnir, M.; Schmidt, E.E.; Hanft, R.W.; Strait, J.B.

    1986-09-12

    The first 16.5 m long SSC dipole magnet (D00001) had its field intensity measured as a function of position with a custom made NMR magnetometer. A short description of the probe is presented. The data obtained (most of it near 2 T spaced apart by one inch) shows an average transfer function of 1.02830 T/KA with position dependent values deviating from the average by up to .00130 T/KA revealing contruction inhomogeneities that were measured with a sensitivity of 25 ppM.

  20. MULTIPLE-QUANTUM NMR IN SOLIDS

    SciTech Connect

    Yen, Y-S.

    1982-11-01

    Time domain multiple-quantum (MQ) nuclear magnetic resonance (NMR) spectroscopy is a powerful tool for spectral simplification and for providing new information on molecular dynamics. In this thesis, applications of MQ NMR are presented and show distinctly the advantages of this method over the conventional single-quantum NMR. Chapter 1 introduces the spin Hamiltonians, the density matrix formalism and some basic concepts of MQ NMR spectroscopy. In chapter 2, {sup 14}N double-quantum coherence is observed with high sensitivity in isotropic solution, using only the magnetization of bound protons. Spin echoes are used to obtain the homogeneous double-quantum spectrum and to suppress a large H{sub 2}O solvent signal. Chapter 3 resolves the main difficulty in observing high MQ transitions in solids. Due to the profusion of spin transitions in a solid, individual lines are unresolved. Excitation and detection of high quantum transitions by normal schemes are thus difficult. To ensure that overlapping lines add constructively and thereby to enhance sensitivity, time-reversal pulse sequences are used to generate all lines in phase. Up to 22-quantum {sup 1}H absorption in solid adamantane is observed. A time dependence study shows an increase in spin correlations as the excitation time increased. In chapter 4, a statistical theory of MQ second moments is developed for coupled spins of spin I = 1/2. The model reveals that the ratio of the average dipolar coupling to the rms value largely determines the dependence of second moments on the number of quanta. The results of this model are checked against computer-calculated and experimental second moments, and show good agreement. A simple scheme is proposed in chapter 5 for sensitivity improvement in a MQ experiment. The scheme involves acquiring all of the signal energy available in the detection period by applying pulsed spinlocking and sampling between pulses. Using this technique on polycrystalline adamantane, a large

  1. Quenched Hydrogen Exchange NMR of Amyloid Fibrils.

    PubMed

    Alexandrescu, Andrei T

    2016-01-01

    Amyloid fibrils are associated with a number of human diseases. These aggregatively misfolded intermolecular β-sheet assemblies constitute some of the most challenging targets in structural biology because to their complexity, size, and insolubility. Here, protocols and controls are described for experiments designed to study hydrogen-bonding in amyloid fibrils indirectly, by transferring information about amide proton occupancy in the fibrils to the dimethyl sulfoxide-denatured state. Since the denatured state is amenable to solution NMR spectroscopy, the method can provide residue-level-resolution data on hydrogen exchange for the monomers that make up the fibrils. PMID:26453215

  2. High resolution 1H NMR of a lipid cubic phase using a solution NMR probe

    NASA Astrophysics Data System (ADS)

    Boyle-Roden, E.; Hoefer, N.; Dey, K. K.; Grandinetti, P. J.; Caffrey, M.

    2007-11-01

    The cubic mesophase formed by monoacylglycerols and water is an important medium for the in meso crystallogenesis of membrane proteins. To investigate molecular level lipid and additive interactions within the cubic phase, a method was developed for improving the resolution of 1H NMR spectra when using a conventional solution state NMR probe. Using this approach we obtained well-resolved J-coupling multiplets in the one-dimensional NMR spectrum of the cubic-Ia3d phase prepared with hydrated monoolein. A high resolution t-ROESY two-dimensional 1H NMR spectrum of the cubic-Ia3d phase is also reported. Using this new methodology, we have investigated the interaction of two additive molecules, L-tryptophan and ruthenium-tris(2,2-bipyridyl) dichloride (rubipy), with the cubic mesophase. Based on the measured chemical shift differences when changing from an aqueous solution to the cubic phase, we conclude that L-tryptophan experiences specific interactions with the bilayer interface, whereas rubipy remains in the aqueous channels and does not associate with the lipid bilayer.

  3. Touch NMR: An NMR Data Processing Application for the iPad

    ERIC Educational Resources Information Center

    Li, Qiyue; Chen, Zhiwei; Yan, Zhiping; Wang, Cheng; Chen, Zhong

    2014-01-01

    Nuclear magnetic resonance (NMR) spectroscopy has become one of the most powerful technologies to aid research in numerous scientific disciplines. With the development of consumer electronics, mobile devices have played increasingly important roles in our daily life. However, there is currently no application available for mobile devices able to…

  4. New generation NMR bioreactor coupled with high-resolution NMR spectroscopy leads to novel discoveries in Moorella thermoaceticum metabolic profiles

    SciTech Connect

    Xue, Junfeng; Isern, Nancy G.; Ewing, R James; Liyu, Andrey V.; Sears, Jesse A.; Knapp, Harlan; Iversen, Jens; Sisk, Daniel R.; Ahring, Birgitte K.; Majors, Paul D.

    2014-06-20

    An in-situ nuclear magnetic resonance (NMR) bioreactor was developed and employed to monitor microbial metabolism under batch-growth conditions in real time. We selected Moorella thermoacetica ATCC 49707 as a test case. M. thermoacetica (formerly Clostridium thermoaceticum) is a strictly anaerobic, thermophilic, acetogenic, gram-positive bacterium with potential for industrial production of chemicals. The metabolic profiles of M. thermoacetica were characterized during growth in batch mode on xylose (a component of lignocellulosic biomass) using the new generation NMR bioreactor in combination with high-resolution, high sensitivity NMR (HR-NMR) spectroscopy. In-situ NMR measurements were performed using water-suppressed H-1 NMR spectroscopy at an NMR frequency of 500 MHz, and aliquots of the bioreactor contents were taken for 600 MHz HR-NMR spectroscopy at specific intervals to confirm metabolite identifications and expand metabolite coverage. M. thermoacetica demonstrated the metabolic potential to produce formate, ethanol and methanol from xylose, in addition to its known capability of producing acetic acid. Real-time monitoring of bioreactor conditions showed a temporary pH decrease, with a concomitant increase in formic acid during exponential growth. Fermentation experiments performed outside of the magnet showed that the strong magnetic field employed for NMR detection did not significantly affect cell metabolism. Use of the in-situ NMR bioreactor facilitated monitoring of the fermentation process in real time, enabling identification of intermediate and end-point metabolites and their correlation with pH and biomass produced during culture growth. Real-time monitoring of culture metabolism using the NMR bioreactor in combination with the HR-NMR spectroscopy will allow optimization of the metabolism of microorganisms producing valuable bioproducts.

  5. NMR assessment on bone simulated under microgravity

    NASA Astrophysics Data System (ADS)

    Ni, Q.; Qin, Y.

    Introduction Microgravity-induced bone loss has been suggested to be similar to disuse-osteoporosis on Earth which constitutes a challenging public health problem No current non-destructive method can provide the microstructural changes in bone particularly on cortical bone Recently the authors have applied low field nuclear magnetic resonance NMR spin-spin relaxation technique and computational analysis method to determine the porosity pore size distribution and microdamage of cortical bone 1-3 The studies by the authors have shown that this technology can be used to characterize microstructural changes as well as bone water distribution bound and mobile water changes of weightless treated simulating a microgravity condition turkey and mouse cortical bone We further determinate that the NMR spin-spin relaxation time T 2 spectrum derived parameters can be used as descriptions of bone quality e g matrix water distribution and porosity size distributions and alone or in combination with current techniques bone mineral density measurements more accurately predict bone mechanical properties Methods underline Bone sample preparation Two kinds of animal samples were collected and prepared for designed experiments from SUNY Cortical bones of the mid-diaphyses of the ulnae of 1-year-old male turkeys were dissected from freshly slaughtered animals Eight samples were categorized from normal or control and four samples were 4-week disuse treated by functionally isolated osteotomies disuse A total of 12

  6. Characterizing carbohydrate-protein interactions by NMR

    PubMed Central

    Bewley, Carole A.; Shahzad-ul-Hussan, Syed

    2013-01-01

    Interactions between proteins and soluble carbohydrates and/or surface displayed glycans are central to countless recognition, attachment and signaling events in biology. The physical chemical features associated with these binding events vary considerably, depending on the biological system of interest. For example, carbohydrate-protein interactions can be stoichiometric or multivalent, the protein receptors can be monomeric or oligomeric, and the specificity of recognition can be highly stringent or rather promiscuous. Equilibrium dissociation constants for carbohydrate binding are known to vary from micromolar to millimolar, with weak interactions being far more prevalent; and individual carbohydrate binding sites can be truly symmetrical or merely homologous, and hence, the affinities of individual sites within a single protein can vary, as can the order of binding. Several factors, including the weak affinities with which glycans bind their protein receptors, the dynamic nature of the glycans themselves, and the non-equivalent interactions among oligomeric carbohydrate receptors, have made NMR an especially powerful tool for studying and defining carbohydrate-protein interactions. Here we describe those NMR approaches that have proven to be the most robust in characterizing these systems, and explain what type of information can (or cannot) be obtained from each. Our goal is to provide to the reader the information necessary for selecting the correct experiment or sets of experiments to characterize their carbohydrate-protein interaction of interest. PMID:23784792

  7. The D0 solenoid NMR magnetometer

    SciTech Connect

    Sten Uldall Hansen Terry Kiper, Tom Regan, John Lofgren et al.

    2002-11-20

    A field monitoring system for the 2 Tesla Solenoid of the D0 detector is described. It is comprised of a very small NMR probe cabled to a DSP based signal processing board. The design magnetic field range is from 1.0 to 2.2 Tesla, corresponding to an RF frequency range of 42.57 to 93.67 MHz. The desired an accuracy is one part in 10{sup 5}. To minimize material in the interaction region of the D0 detector, the overall thickness of the NMR probe is 4 mm, including its mounting plate, and its width is 10 mm. To minimize cable mass, 4mm diameter IMR-100A cables are used for transmitting the RF signals from a nearby patch panel 25 meters to each of four probes mounted within the bore of the solenoid. RG213U cables 45 meters long are used to send the RF from the movable counting house to the patch panel. With this setup, the detector signal voltage at the moving counting room is in the range of 250-400 mV.

  8. Algorithmic cooling and scalable NMR quantum computers

    PubMed Central

    Boykin, P. Oscar; Mor, Tal; Roychowdhury, Vwani; Vatan, Farrokh; Vrijen, Rutger

    2002-01-01

    We present here algorithmic cooling (via polarization heat bath)—a powerful method for obtaining a large number of highly polarized spins in liquid nuclear-spin systems at finite temperature. Given that spin-half states represent (quantum) bits, algorithmic cooling cleans dirty bits beyond the Shannon's bound on data compression, by using a set of rapidly thermal-relaxing bits. Such auxiliary bits could be implemented by using spins that rapidly get into thermal equilibrium with the environment, e.g., electron spins. Interestingly, the interaction with the environment, usually a most undesired interaction, is used here to our benefit, allowing a cooling mechanism. Cooling spins to a very low temperature without cooling the environment could lead to a breakthrough in NMR experiments, and our “spin-refrigerating” method suggests that this is possible. The scaling of NMR ensemble computers is currently one of the main obstacles to building larger-scale quantum computing devices, and our spin-refrigerating method suggests that this problem can be resolved. PMID:11904402

  9. Assessment of Bone Microstructural Changes by NMR

    NASA Astrophysics Data System (ADS)

    Ni, Qingwen; Wang, Xiaodu

    2008-03-01

    Previous studies have shown that age related increases in bone porosity without significant changes in bone mineral density (BMD) (without bone microstructural information) result in a decrease in bone strength. Bone fracture toughness is also significantly correlated to changes in porosity, microarchitecture, collagen integrity, microdamage, and water distribution, all of which are measures of bone quality. Unfortunately, current technology does not allow the non-destructive and non-invasive detection of bone water distribution or other measures of bone quality including microporosity. On the other hand, Nuclear Magnetic Resonance (NMR) proton spin-spin (T2) relaxation time measurements and computational analytical method have been used to determine microstructural characteristics of various types of fluid filled porous materials. The study in here is to demonstrate that non-destructive and non-invasive NMR proton spin-spin (T2) relaxation techniques has been developed and applied to quantify the porosity, pore size distribution and water distribution in human cortical bone. This new bone microstructural information can then be used as descriptions of bone quality and, along or in combination with existing method (BMD) to more accurately assess bone fracture risk, and the results could help doctors and researchers to detect osteoporosis and other conditions related to weak bones in persons.

  10. NMR crystallography: the use of chemical shifts

    NASA Astrophysics Data System (ADS)

    Harris, Robin K.

    2004-10-01

    Measurements of chemical shifts obtained from magic-angle spinning NMR spectra (together with quantum mechanical computations of shielding) can provide valuable information on crystallography. Examples are given of the determination of crystallographic asymmetric units, of molecular symmetry in the solid-state environment, and of crystallographic space group assignment. Measurements of full tensor components for 199Hg have given additional coordination information. The nature of intermolecular hydrogen bonding in cortisone acetate polymorphs and solvates is obtained from chemical shift information, also involving measurement of the full tensor parameters. The resulting data have been used as restraints, built into the computation algorithm, in the analysis of powder diffraction patterns to give full crystal structures. A combination of quantum mechanical computation of shielding and measurement of proton chemical shifts (obtained by high-speed MAS) leads to the determination of the position of a proton in an intermolecular hydrogen bond. A recently-developed computer program specifically based on crystallographic repetition has been shown to give acceptable results. Moreover, NMR chemical shifts can distinguish between static and dynamic disorder in crystalline materials and can be used to determine modes and rates of molecular exchange motion.

  11. Methods for spatial localization in NMR

    SciTech Connect

    Rath, A.R.

    1985-01-01

    Several unique coil configurations were developed that have applications in nuclear magnetic resonance. These include a number of designs appropriate for use as rf surface coils, and two configurations developed as NMR magnets. The magnetic field profiles were calculated for each of these designs, from which field strength and homogeneity information were obtained. The rf coil configurations modelled include the opposed loop, opposed half loop, bicycle wheel, opposed bicycle wheel, and semi-toroid. The opposed loop design was studied in detail in terms of the theoretical spatial sensitivity and selectivity it offers. A number of NMR experiments were performed to test the validity of these theoretical calculations. This configuration produces a field that is substantially reduced near the coil itself, compared with the field produced by a single loop surface coil, but that rises to a maximum along the coil axis yielding a somewhat homogeneous region that may be used to achieve a degree of spatial localization. Several comparison schemes are used to evaluate the relative advantages and disadvantages of both the single loop and the opposed loop coil. The opposed coil concept also has been applied to the design of magnets. The results of calculations on the homogeneity and field strength possible with an opposed solenoid magnet are presented.

  12. NMR measurements in solutions of dialkylimidazolium haloaluminates

    SciTech Connect

    Takahashi, S.; Saboungi, M.L.; Klingler, R.J.; Chen, M.J.; Rathke, J.W.

    1992-06-01

    {sup 27}Al and {sup 35}Cl NMR spectra of AlCl{sub 3}-1-ethyl-3-methyl imidazolium chloride (EMIC) melts were measured for initial compositions ranging from 50 to 67 mol % AlCl{sub 3} at various temperatures. It was shown by changing the preaquisition delay time (DE value) that the dominant aluminum species are AlCl{sub 4}{sup {minus}} in the melt formed by mixing 50 mol % with EMIC and Al{sub 2}Cl{sub 7}{sup {minus}} in the 67 mol % AlCl{sub 3} melt. In the equimolar mixture, the chemical shift of {sup 27}Al NMR spectrum is 103.28 ppm and the line width is 22.83Hz. In the 67 mol % AlCl{sub 3} mixture, the chemical shift is 103.41 ppm and the line width is 2624Hz. A third species observed at 97 ppm in the {sup 27}Al spectra for the 55 and 60 mol % AlCl{sub 3} mixtures is identified to be a product of the reaction with residual water. The relaxation rates for each species in the melts were determined.

  13. CHARACTERIZATION OF METABOLITES IN SMALL FISH BIOFLUIDS AND TISSUES BY NMR SPECTROSCOPY

    EPA Science Inventory

    Nuclear magnetic resonance (NMR) spectroscopy has been utilized for assessing ecotoxicity in small fish models by means of metabolomics. Two fundamental challenges of NMR-based metabolomics are the detection limit and characterization of metabolites (or NMR resonance assignments...

  14. NMR of platinum catalysts: Double NMR of chemisorbed carbon monoxide and a model for the platinum NMR line shape

    SciTech Connect

    Makowka, C.D.; Slichter, C.P. ); Sinfelt, J.H. )

    1985-05-01

    The authors report observation of the NMR line of {sup 195}Pt atoms in the surface layer of small platinum-metal particles on which {sup 13}CO has been chemisorbed. The surface {sup 195}Pt atoms are resolved from those of {sup 195}Pt atoms deeper in the particle by spin-echo double resonance between {sup 195}Pt and {sup 13}C. The particles, supported on {eta}-alumina, had dispersions (fraction of the atoms that are on the surface) of 26% and 76%. Comparison with {sup 195}Pt resonance in Pt carbonyls suggests that the magnitude of the Knight shift of the surface Pt is less than 0.2%. Analysis of the {sup 195}Pt spin-lattice relaxation indicates that the small surface Knight shift results from cancellation of 6s and 5d core-polarization contributions as was found theoretically by Weinert and Freeman for clean Pt surfaces. The {sup 13}C-{sup 195}Pt indirect spin coupling is found to be very similar to those in diamagnetic platinum carbonyl molecules. The results show that CO bonds via the C atom and verify that concepts from studies of large single crystals are valid for the small particles. The key features of the {sup 195}Pt line shapes in these small platinum particles are described by a simple phenomenological model of the spatial Knight-shift variation inside these particles. The model successfully describes the major structure seen in the NMR line shapes of samples with dispersions ranging from 5% to 76%.

  15. Probe for high resolution NMR with sample reorientation

    DOEpatents

    Pines, A.; Samoson, A.

    1990-02-06

    An improved NMR probe and method are described which substantially improve the resolution of NMR measurements made on powdered or amorphous or otherwise orientationally disordered samples. The apparatus mechanically varies the orientation of the sample such that the time average of two or more sets of spherical harmonic functions are zero. 8 figs.

  16. Chemical Equilibrium in Supramolecular Systems as Studied by NMR Spectrometry

    ERIC Educational Resources Information Center

    Gonzalez-Gaitano, Gustavo; Tardajos, Gloria

    2004-01-01

    Undergraduate students are required to study the chemical balance in supramolecular assemblies constituting two or more interacting species, by using proton NMR spectrometry. A good knowledge of physical chemistry, fundamentals of chemical balance, and NMR are pre-requisites for conducting this study.

  17. Structure calculation, refinement and validation using CcpNmr Analysis

    PubMed Central

    Skinner, Simon P.; Goult, Benjamin T.; Fogh, Rasmus H.; Boucher, Wayne; Stevens, Tim J.; Laue, Ernest D.; Vuister, Geerten W.

    2015-01-01

    CcpNmr Analysis provides a streamlined pipeline for both NMR chemical shift assignment and structure determination of biological macromolecules. In addition, it encompasses tools to analyse the many additional experiments that make NMR such a pivotal technique for research into complex biological questions. This report describes how CcpNmr Analysis can seamlessly link together all of the tasks in the NMR structure-determination process. It details each of the stages from generating NMR restraints [distance, dihedral, hydrogen bonds and residual dipolar couplings (RDCs)], exporting these to and subsequently re-importing them from structure-calculation software (such as the programs CYANA or ARIA) and analysing and validating the results obtained from the structure calculation to, ultimately, the streamlined deposition of the completed assignments and the refined ensemble of structures into the PDBe repository. Until recently, such solution-structure determination by NMR has been quite a laborious task, requiring multiple stages and programs. However, with the new enhancements to CcpNmr Analysis described here, this process is now much more intuitive and efficient and less error-prone. PMID:25615869

  18. Heteronuclear Multidimensional Protein NMR in a Teaching Laboratory

    ERIC Educational Resources Information Center

    Wright, Nathan T.

    2016-01-01

    Heteronuclear multidimensional NMR techniques are commonly used to study protein structure, function, and dynamics, yet they are rarely taught at the undergraduate level. Here, we describe a senior undergraduate laboratory where students collect, process, and analyze heteronuclear multidimensional NMR experiments using an unstudied Ig domain (Ig2…

  19. Probe for high resolution NMR with sample reorientation

    DOEpatents

    Pines, Alexander; Samoson, Ago

    1990-01-01

    An improved NMR probe and method are described which substantially improve the resolution of NMR measurements made on powdered or amorphous or otherwise orientationally disordered samples. The apparatus mechanically varies the orientation of the sample such that the time average of two or more sets of spherical harmonic functions are zero.

  20. Straightforward and complete deposition of NMR data to the PDBe.

    PubMed

    Penkett, Christopher J; van Ginkel, Glen; Velankar, Sameer; Swaminathan, Jawahar; Ulrich, Eldon L; Mading, Steve; Stevens, Tim J; Fogh, Rasmus H; Gutmanas, Aleksandras; Kleywegt, Gerard J; Henrick, Kim; Vranken, Wim F

    2010-10-01

    We present a suite of software for the complete and easy deposition of NMR data to the PDB and BMRB. This suite uses the CCPN framework and introduces a freely downloadable, graphical desktop application called CcpNmr Entry Completion Interface (ECI) for the secure editing of experimental information and associated datasets through the lifetime of an NMR project. CCPN projects can be created within the CcpNmr Analysis software or by importing existing NMR data files using the CcpNmr FormatConverter. After further data entry and checking with the ECI, the project can then be rapidly deposited to the PDBe using AutoDep, or exported as a complete deposition NMR-STAR file. In full CCPN projects created with ECI, it is straightforward to select chemical shift lists, restraint data sets, structural ensembles and all relevant associated experimental collection details, which all are or will become mandatory when depositing to the PDB. Instructions and download information for the ECI are available from the PDBe web site at http://www.ebi.ac.uk/pdbe/nmr/deposition/eci.html . PMID:20680401

  1. Fluid-Rock Characterization and Interactions in NMR Well Logging

    SciTech Connect

    George J. Hirasaki; Kishore K. Mohanty

    2005-09-05

    The objective of this report is to characterize the fluid properties and fluid-rock interactions that are needed for formation evaluation by NMR well logging. The advances made in the understanding of NMR fluid properties are summarized in a chapter written for an AAPG book on NMR well logging. This includes live oils, viscous oils, natural gas mixtures, and the relation between relaxation time and diffusivity. Oil based drilling fluids can have an adverse effect on NMR well logging if it alters the wettability of the formation. The effect of various surfactants on wettability and surface relaxivity are evaluated for silica sand. The relation between the relaxation time and diffusivity distinguishes the response of brine, oil, and gas in a NMR well log. A new NMR pulse sequence in the presence of a field gradient and a new inversion technique enables the T{sub 2} and diffusivity distributions to be displayed as a two-dimensional map. The objectives of pore morphology and rock characterization are to identify vug connectivity by using X-ray CT scan, and to improve NMR permeability correlation. Improved estimation of permeability from NMR response is possible by using estimated tortuosity as a parameter to interpolate between two existing permeability models.

  2. {sup 17}O NMR investigations of oxidative degradation in polymers

    SciTech Connect

    Alam, T.M.; Celina, M.; Assink, R.A.; Gillen, K.T.; Clough, R.L.

    1996-12-31

    We have initiated studies using both solution and solid state magic angle spinning {sup 17}O NMR for a series of oxidatively aged polymers. This short note reports the solution {sup 17}O NMR for oxidatively degraded polypropylene, ethylene-propylene-diene, polyisoprene, and nitrile rubber. Enriched O{sub 2} is used during the accelerated aging. 3 figs, 7 refs.

  3. NMR-Metabolic Methodology in the Study of GM Foods

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The 1H NMR methodology used in the study of genetically modified (GM) foodstuff is discussed. The study of transgenic lettuce (Lactuca sativa cv "Luxor") over-expressing the KNAT1 gene from Arabidopsis is presented as a novel study-case. The 1H NMR metabolic profiling was carried out. Twenty-two wat...

  4. Functional groups identified by solid state 13C NMR spectroscopy

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Animal manure is generally high in organic matter intensity so it is well suitable for 13C nuclear magnetic resonance (NMR) analysis. Solid-state 13C NMR techniques used in characterizing organic matter and its components include, but are not limited to, cross-polarization /magic angle spinning (CP...

  5. Two-dimensional NMR spectroscopy. Applications for chemists and biochemists

    SciTech Connect

    Croasmun, W.R.; Carlson, R.M.K.

    1987-01-01

    Two-dimensional nuclear magnetic resonance spectroscopy (2-D NMR) has become a very powerful class of experiments (in the hands of an adept scientist) with broad adaptability to new situations. It is the product of a happy marriage between modern pulse FT-NMR technology, with its large memory and high-speed computers, and the physicists and chemists who love to manipulate spin systems. Basic 2-D experiments are now a standard capability of modern NMR spectrometers, and this timely book intends to make 2-D NMR users of those who are familiar with normal 1-D NMR. The 2-D NMR goal is correlation of the lines of the observed NMR spectrum with other properties of the system. This book deals with applications to high-resolution spectrum analysis, utilizing either coupling between the NMR-active nuclei or chemical exchange to perform the correlation. The coupling can be scalar (through bonds) or direct through space (within 5 A). The coupling may be homonuclear (between like nuclei) or heteronuclear.

  6. New generation NMR bioreactor coupled with high-resolution NMR spectroscopy leads to novel discoveries in Moorella thermoacetica metabolic profiles.

    PubMed

    Xue, Junfeng; Isern, Nancy G; Ewing, R James; Liyu, Andrei V; Sears, Jesse A; Knapp, Harlan; Iversen, Jens; Sisk, Daniel R; Ahring, Birgitte K; Majors, Paul D

    2014-10-01

    An in situ nuclear magnetic resonance (NMR) bioreactor was developed and employed to monitor microbial metabolism under batch growth conditions in real time. We selected Moorella thermoacetica ATCC 49707 as a test case. M. thermoacetica (formerly Clostridium thermoaceticum) is a strictly anaerobic, thermophilic, acetogenic, gram-positive bacterium with potential for industrial production of chemicals. The metabolic profiles of M. thermoacetica were characterized during growth in batch mode on xylose (a component of lignocellulosic biomass) using the new generation NMR bioreactor in combination with high-resolution NMR (HR-NMR) spectroscopy. In situ NMR measurements were performed using water-suppressed H-1 NMR spectroscopy at 500 MHz, and aliquots of the bioreactor contents were taken for 600-MHz HR-NMR spectroscopy at specific intervals to confirm metabolite identifications and expand metabolite coverage. M. thermoacetica demonstrated the metabolic potential to produce formate, ethanol, and methanol from xylose, in addition to its known capability of producing acetic acid. Real-time monitoring of bioreactor conditions showed a temporary pH decrease, with a concomitant increase in formic acid during exponential growth. Fermentation experiments performed outside of the magnet showed that the strong magnetic field employed for NMR detection did not significantly affect cell metabolism. Use of the in situ NMR bioreactor facilitated monitoring of the fermentation process, enabling identification of intermediate and endpoint metabolites and their correlation with pH and biomass produced during culture growth. Real-time monitoring of culture metabolism using the NMR bioreactor in combination with HR-NMR spectroscopy will allow optimization of the metabolism of microorganisms producing valuable bioproducts. PMID:24946863

  7. Facing and Overcoming Sensitivity Challenges in Biomolecular NMR Spectroscopy.

    PubMed

    Ardenkjaer-Larsen, Jan-Henrik; Boebinger, Gregory S; Comment, Arnaud; Duckett, Simon; Edison, Arthur S; Engelke, Frank; Griesinger, Christian; Griffin, Robert G; Hilty, Christian; Maeda, Hidaeki; Parigi, Giacomo; Prisner, Thomas; Ravera, Enrico; van Bentum, Jan; Vega, Shimon; Webb, Andrew; Luchinat, Claudio; Schwalbe, Harald; Frydman, Lucio

    2015-08-01

    In the Spring of 2013, NMR spectroscopists convened at the Weizmann Institute in Israel to brainstorm on approaches to improve the sensitivity of NMR experiments, particularly when applied in biomolecular settings. This multi-author interdisciplinary Review presents a state-of-the-art description of the primary approaches that were considered. Topics discussed included the future of ultrahigh-field NMR systems, emerging NMR detection technologies, new approaches to nuclear hyperpolarization, and progress in sample preparation. All of these are orthogonal efforts, whose gains could multiply and thereby enhance the sensitivity of solid- and liquid-state experiments. While substantial advances have been made in all these areas, numerous challenges remain in the quest of endowing NMR spectroscopy with the sensitivity that has characterized forms of spectroscopies based on electrical or optical measurements. These challenges, and the ways by which scientists and engineers are striving to solve them, are also addressed. PMID:26136394

  8. Synchronous Spin Exchange Optical Pumping for Precision NMR

    NASA Astrophysics Data System (ADS)

    Korver, Anna; Weber, Josh; Thrasher, Daniel; Walker, Thad

    2016-05-01

    We present the successful execution of synchronous spin exchange optical pumping for precision NMR. In this novel form of NMR, the bias field is applied as a sequence of alkali 2 π pulses; the resulting transverse alkali polarization is then modulated at the NMR frequency and spin exchange collisions build up a transverse precessing noble gas polarization. As compared to longitudinally pumped NMR, this method suppresses the alkali frequency shift by over a factor of 2500. We also discuss how we use synchronous spin exchange optical pumping to excite two noble gas species simultaneously. With dual species operation, we are able to use one species to lock the magnetic field while the other is left to detect nonmagnetic interactions. This method promises to achieve NMR frequency uncertainties of 100nHz/√{ Hz}. Research supported by the NSF and Northrop-Grumman Corp.

  9. Studies of organic paint binders by NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Spyros, A.; Anglos, D.

    2006-06-01

    Nuclear magnetic resonance spectroscopy is applied to the study of aged binding media used in paintings, namely linseed oil, egg tempera and an acrylic medium. High resolution 1D and 2D NMR experiments establish the state of hydrolysis and oxidation of the linseed and egg tempera binders after five years of aging, by determining several markers sensitive to the hydrolytic and oxidative processes of the binder lipid fraction. The composition of the acrylic binder co-polymer is determined by 2D NMR spectroscopy, while the identification of a surfactant, poly(ethylene glycol), found in greater amounts in aged acrylic medium, is reported. The non-destructive nature of the proposed analytical NMR methodology, and minimization of the amount of binder material needed through the use of sophisticated cryoprobes and hyphenated LC-NMR techniques, make NMR attractive for the arts analyst, in view of its rapid nature and experimental simplicity.

  10. Membrane Protein Structure and Dynamics from NMR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Hong, Mei; Zhang, Yuan; Hu, Fanghao

    2012-05-01

    We review the current state of membrane protein structure determination using solid-state nuclear magnetic resonance (NMR) spectroscopy. Multidimensional magic-angle-spinning correlation NMR combined with oriented-sample experiments has made it possible to measure a full panel of structural constraints of membrane proteins directly in lipid bilayers. These constraints include torsion angles, interatomic distances, oligomeric structure, protein dynamics, ligand structure and dynamics, and protein orientation and depth of insertion in the lipid bilayer. Using solid-state NMR, researchers have studied potassium channels, proton channels, Ca2+ pumps, G protein-coupled receptors, bacterial outer membrane proteins, and viral fusion proteins to elucidate their mechanisms of action. Many of these membrane proteins have also been investigated in detergent micelles using solution NMR. Comparison of the solid-state and solution NMR structures provides important insights into the effects of the solubilizing environment on membrane protein structure and dynamics.

  11. Introducing the gNMR Program in an Introductory NMR Spectrometry Course to Parallel Its Use by Spectroscopists

    ERIC Educational Resources Information Center

    Rummey, Jackie M.; Boyce, Mary C.

    2004-01-01

    An approach that is useful to any introductory nuclear magnetic resonance (NMR) spectroscopy course is developed. This approach to teaching NMR spectrometry includes spectral simulation along with the traditional elements of hands-on instrument use and structure elucidation to demonstrate the connection between simulating a spectrum and structure…

  12. Multiplexed NMR: An Automated CapNMR Dual-Sample Probe

    PubMed Central

    Norcross, James A.; Milling, Craig T.; Olson, Dean L.; Xu, Duanxiang; Audrieth, Anthony; Albrecht, Robert; Ruan, Ke; Likos, John; Jones, Claude; Peck, Timothy L.

    2010-01-01

    A new generation of micro-scale, nuclear magnetic resonance (CapNMR™) probe technology employs two independent detection elements to accommodate two samples simultaneously. Each detection element in the Dual-Sample CapNMR Probe (DSP) delivers the same spectral resolution and S/N as in a CapNMR probe configured to accommodate one sample at a time. A high degree of electrical isolation allows the DSP to be used in a variety of data acquisition modes. Both samples are shimmed simultaneously to achieve high spectral resolution for simultaneous data acquisition, or alternatively, a flowcell-specific shim set is readily called via spectrometer subroutines to enable acquisition from one sample while the other is being loaded. An automation system accommodates loading of two samples via dual injection ports on an autosampler and two completely independent flowpaths leading to dedicated flowcells in the DSP probe. PMID:20681560

  13. NMR Measurements of Granular Flow and Compaction

    NASA Astrophysics Data System (ADS)

    Fukushima, Eiichi

    1998-03-01

    Nuclear magnetic resonance (NMR) can be used to measure statistical distributions of granular flow velocity and fluctuations of velocity, as well as spatial distributions of particulate concentration, flow velocity, its fluctuations, and other parameters that may be derived from these. All measurements have been of protons in liquid-containing particles such as mustard seeds or pharmaceutical pills. Our favorite geometry has been the slowly rotating partially filled rotating drum with granular flow taking place along the free surface of the particles. All the above-mentioned parameters have been studied as well as a spatial distribution of particulate diffusion coefficients, energy dissipation due to collisions, as well as segregation of non-uniform mixtures of granular material. Finally, we describe some motions of granular material under periodic vibrations.

  14. NMR local coil with adjustable spacing

    SciTech Connect

    Dembinski, G.T.

    1988-03-22

    A local coil assembly for use in NMR imaging is described which comprises: a base; a first local coil module mounted to the base and extending upward therefrom; sockets disposed in the base, each at a different distance from the first local coil module; a second local coil module having a connector therein which mates with each of the sockets to enable the second local coil module to be connected to the base at any one of the sockets; and a set of reactive components. The values of the respective reactive components are selected such that the second local oil module may be connected to any of the sockets without any substantial change in the resonant frequency of the assembly.

  15. Two-Dimensional NMR Lineshape Analysis

    PubMed Central

    Waudby, Christopher A.; Ramos, Andres; Cabrita, Lisa D.; Christodoulou, John

    2016-01-01

    NMR titration experiments are a rich source of structural, mechanistic, thermodynamic and kinetic information on biomolecular interactions, which can be extracted through the quantitative analysis of resonance lineshapes. However, applications of such analyses are frequently limited by peak overlap inherent to complex biomolecular systems. Moreover, systematic errors may arise due to the analysis of two-dimensional data using theoretical frameworks developed for one-dimensional experiments. Here we introduce a more accurate and convenient method for the analysis of such data, based on the direct quantum mechanical simulation and fitting of entire two-dimensional experiments, which we implement in a new software tool, TITAN (TITration ANalysis). We expect the approach, which we demonstrate for a variety of protein-protein and protein-ligand interactions, to be particularly useful in providing information on multi-step or multi-component interactions. PMID:27109776

  16. Exploring RNA polymerase regulation by NMR spectroscopy

    PubMed Central

    Drögemüller, Johanna; Strauß, Martin; Schweimer, Kristian; Wöhrl, Birgitta M.; Knauer, Stefan H.; Rösch, Paul

    2015-01-01

    RNA synthesis is a central process in all organisms, with RNA polymerase (RNAP) as the key enzyme. Multisubunit RNAPs are evolutionary related and are tightly regulated by a multitude of transcription factors. Although Escherichia coli RNAP has been studied extensively, only little information is available about its dynamics and transient interactions. This information, however, are crucial for the complete understanding of transcription regulation in atomic detail. To study RNAP by NMR spectroscopy we developed a highly efficient procedure for the assembly of active RNAP from separately expressed subunits that allows specific labeling of the individual constituents. We recorded [1H,13C] correlation spectra of isoleucine, leucine, and valine methyl groups of complete RNAP and the separately labeled β’ subunit within reconstituted RNAP. We further produced all RNAP subunits individually, established experiments to determine which RNAP subunit a certain regulator binds to, and identified the β subunit to bind NusE. PMID:26043358

  17. Two-Dimensional NMR Lineshape Analysis.

    PubMed

    Waudby, Christopher A; Ramos, Andres; Cabrita, Lisa D; Christodoulou, John

    2016-01-01

    NMR titration experiments are a rich source of structural, mechanistic, thermodynamic and kinetic information on biomolecular interactions, which can be extracted through the quantitative analysis of resonance lineshapes. However, applications of such analyses are frequently limited by peak overlap inherent to complex biomolecular systems. Moreover, systematic errors may arise due to the analysis of two-dimensional data using theoretical frameworks developed for one-dimensional experiments. Here we introduce a more accurate and convenient method for the analysis of such data, based on the direct quantum mechanical simulation and fitting of entire two-dimensional experiments, which we implement in a new software tool, TITAN (TITration ANalysis). We expect the approach, which we demonstrate for a variety of protein-protein and protein-ligand interactions, to be particularly useful in providing information on multi-step or multi-component interactions. PMID:27109776

  18. Spatially resolved spectroscopy using tapered stripline NMR

    NASA Astrophysics Data System (ADS)

    Tijssen, Koen C. H.; Bart, Jacob; Tiggelaar, Roald M.; Janssen, J. W. G. (Hans); Kentgens, Arno P. M.; van Bentum, P. Jan M.

    2016-02-01

    Magnetic field B0 gradients are essential in modern Nuclear Magnetic Resonance spectroscopy and imaging. Although RF/B1 gradients can be used to fulfill a similar role, this is not used in common practice because of practical limitations in the design of B1 gradient coils. Here we present a new method to create B1 gradients using stripline RF coils. The conductor-width of a stripline NMR chip and the strength of its radiofrequency field are correlated, so a stripline chip can be tapered to produce any arbitrary shaped B1 field gradient. Here we show the characterization of this tapered stripline configuration and demonstrate three applications: magnetic resonance imaging on samples with nL-μL volumes, reaction monitoring of fast chemical reactions (10-2-101 s) and the compensation of B0 field gradients to obtain high-resolution spectra in inhomogeneous magnetic fields.

  19. NMR solvent peak suppression by nonlinear excitation

    NASA Astrophysics Data System (ADS)

    Levitt, Malcolm H.

    1988-03-01

    Most existing NMR solvent peak suppression sequences provide a satisfactory dependence of the intensity of excited signals on frequency but poor phase characteristics. In practice this leads to spectral distortions which generally become more severe as the frequency selectivity of the sequence is increased. However, it is shown that by working well outside the linear response regime, excitation schemes which combine high frequency selectivity with good phase properties may be devised. Sequences of six rectangular radio-frequency pulses were discovered using a combination of coherent averaging theory to treat the near-resonant behavior and numerical simulation further from resonance. Extensive use of symmetry greatly simplifies both the coherent averaging calculations and the numerical simulations. The new pulse sequences have been given the acronym NERO (nonlinear excitation rejecting on-resonance). Experimental spectra of an enzyme in dilute aqueous solution are shown.

  20. Improved nuclear magnetic resonance apparatus having semitoroidal rf coil for use in topical NMR and NMR imaging

    DOEpatents

    Fukushima, E.; Roeder, S.B.W.; Assink, R.A.; Gibson, A.A.V.

    1984-01-01

    An improved nuclear magnetic resonance (NMR) apparatus for use in topical magnetic resonance (TMR) spectroscopy and other remote sensing NMR applications includes a semitoroidal radio frequency (rf) coil. The semitoroidal rf coil produces an effective alternating magnetic field at a distance from the poles of the coil, so as to enable NMR measurements to be taken from selected regions inside an object, particularly including human and other living subjects. The semitoroidal rf coil is relatively insensitive to magnetic interference from metallic objects located behind the coil, thereby rendering the coil particularly suited for use in both conventional and superconducting NMR magnets. The semitoroidal NMR coil can be constructed so that it emits little or no excess rf electric field associated with the rf magnetic field, thus avoiding adverse effects due to dielectric heating of the sample or to any other interaction of the electric field with the sample.

  1. ImatraNMR: novel software for batch integration and analysis of quantitative NMR spectra.

    PubMed

    Mäkelä, A V; Heikkilä, O; Kilpeläinen, I; Heikkinen, S

    2011-08-01

    Quantitative NMR spectroscopy is a useful and important tool for analysis of various mixtures. Recently, in addition of traditional quantitative 1D (1)H and (13)C NMR methods, a variety of pulse sequences aimed for quantitative or semiquantitative analysis have been developed. To obtain actual usable results from quantitative spectra, they must be processed and analyzed with suitable software. Currently, there are many processing packages available from spectrometer manufacturers and third party developers, and most of them are capable of analyzing and integration of quantitative spectra. However, they are mainly aimed for processing single or few spectra, and are slow and difficult to use when large numbers of spectra and signals are being analyzed, even when using pre-saved integration areas or custom scripting features. In this article, we present a novel software, ImatraNMR, designed for batch analysis of quantitative spectra. In addition to capability of analyzing large number of spectra, it provides results in text and CSV formats, allowing further data-analysis using spreadsheet programs or general analysis programs, such as Matlab. The software is written with Java, and thus it should run in any platform capable of providing Java Runtime Environment version 1.6 or newer, however, currently it has only been tested with Windows and Linux (Ubuntu 10.04). The software is free for non-commercial use, and is provided with source code upon request. PMID:21705250

  2. ImatraNMR: Novel software for batch integration and analysis of quantitative NMR spectra

    NASA Astrophysics Data System (ADS)

    Mäkelä, A. V.; Heikkilä, O.; Kilpeläinen, I.; Heikkinen, S.

    2011-08-01

    Quantitative NMR spectroscopy is a useful and important tool for analysis of various mixtures. Recently, in addition of traditional quantitative 1D 1H and 13C NMR methods, a variety of pulse sequences aimed for quantitative or semiquantitative analysis have been developed. To obtain actual usable results from quantitative spectra, they must be processed and analyzed with suitable software. Currently, there are many processing packages available from spectrometer manufacturers and third party developers, and most of them are capable of analyzing and integration of quantitative spectra. However, they are mainly aimed for processing single or few spectra, and are slow and difficult to use when large numbers of spectra and signals are being analyzed, even when using pre-saved integration areas or custom scripting features. In this article, we present a novel software, ImatraNMR, designed for batch analysis of quantitative spectra. In addition to capability of analyzing large number of spectra, it provides results in text and CSV formats, allowing further data-analysis using spreadsheet programs or general analysis programs, such as Matlab. The software is written with Java, and thus it should run in any platform capable of providing Java Runtime Environment version 1.6 or newer, however, currently it has only been tested with Windows and Linux (Ubuntu 10.04). The software is free for non-commercial use, and is provided with source code upon request.

  3. Internet Technology in Magnetic Resonance: A Common Gateway Interface Program for the World-Wide Web NMR Spectrometer

    NASA Astrophysics Data System (ADS)

    Buszko, Marian L.; Buszko, Dominik; Wang, Daniel C.

    1998-04-01

    A custom-written Common Gateway Interface (CGI) program for remote control of an NMR spectrometer using a World Wide Web browser has been described. The program, running on a UNIX workstation, uses multiple processes to handle concurrent tasks of interacting with the user and with the spectrometer. The program's parent process communicates with the browser and sends out commands to the spectrometer; the child process is mainly responsible for data acquisition. Communication between the processes is via the shared memory mechanism. The WWW pages that have been developed for the system make use of the frames feature of web browsers. The CGI program provides an intuitive user interface to the NMR spectrometer, making, in effect, a complex system an easy-to-use Web appliance.

  4. Can NMR solve some significant challenges in metabolomics?

    NASA Astrophysics Data System (ADS)

    Nagana Gowda, G. A.; Raftery, Daniel

    2015-11-01

    The field of metabolomics continues to witness rapid growth driven by fundamental studies, methods development, and applications in a number of disciplines that include biomedical science, plant and nutrition sciences, drug development, energy and environmental sciences, toxicology, etc. NMR spectroscopy is one of the two most widely used analytical platforms in the metabolomics field, along with mass spectrometry (MS). NMR's excellent reproducibility and quantitative accuracy, its ability to identify structures of unknown metabolites, its capacity to generate metabolite profiles using intact bio-specimens with no need for separation, and its capabilities for tracing metabolic pathways using isotope labeled substrates offer unique strengths for metabolomics applications. However, NMR's limited sensitivity and resolution continue to pose a major challenge and have restricted both the number and the quantitative accuracy of metabolites analyzed by NMR. Further, the analysis of highly complex biological samples has increased the demand for new methods with improved detection, better unknown identification, and more accurate quantitation of larger numbers of metabolites. Recent efforts have contributed significant improvements in these areas, and have thereby enhanced the pool of routinely quantifiable metabolites. Additionally, efforts focused on combining NMR and MS promise opportunities to exploit the combined strength of the two analytical platforms for direct comparison of the metabolite data, unknown identification and reliable biomarker discovery that continue to challenge the metabolomics field. This article presents our perspectives on the emerging trends in NMR-based metabolomics and NMR's continuing role in the field with an emphasis on recent and ongoing research from our laboratory.

  5. High-resolution NMR spectroscopy under the fume hood.

    PubMed

    Küster, Simon K; Danieli, Ernesto; Blümich, Bernhard; Casanova, Federico

    2011-08-01

    This work reports the possibility to acquire high-resolution (1)H NMR spectra with a fist-sized NMR magnet directly installed under the fume hood. The small NMR sensor based on permanent magnets was used to monitor the trimerization of propionaldehyde catalyzed by indium trichloride in real time by continuously circulating the reaction mixture through the magnet bore in a closed loop with the help of a peristaltic pump. Thanks to the chemical selectivity of NMR spectroscopy the progress of the reaction can be monitored on-line by determining the concentrations of both reactant and product from the area under their respective lines in the NMR spectra as a function of time. This in situ measurement demonstrates that NMR probes can be used in chemistry laboratories, e.g. for reaction optimization, or installed at specific points of interest along industrial process lines. Therefore, it will open the door for the implementation of feedback control based on spectroscopic NMR data. PMID:21698335

  6. NMR data visualization, processing, and analysis on mobile devices.

    PubMed

    Cobas, Carlos; Iglesias, Isaac; Seoane, Felipe

    2015-08-01

    Touch-screen computers are emerging as a popular platform for many applications, including those in chemistry and analytical sciences. In this work, we present our implementation of a new NMR 'app' designed for hand-held and portable touch-controlled devices, such as smartphones and tablets. It features a flexible architecture formed by a powerful NMR processing and analysis kernel and an intuitive user interface that makes full use of the smart devices haptic capabilities. Routine 1D and 2D NMR spectra acquired in most NMR instruments can be processed in a fully unattended way. More advanced experiments such as non-uniform sampled NMR spectra are also supported through a very efficient parallelized Modified Iterative Soft Thresholding algorithm. Specific technical development features as well as the overall feasibility of using NMR software apps will also be discussed. All aspects considered the functionalities of the app allowing it to work as a stand-alone tool or as a 'companion' to more advanced desktop applications such as Mnova NMR. PMID:25924947

  7. Benchmarking NMR experiments: A relational database of protein pulse sequences

    NASA Astrophysics Data System (ADS)

    Senthamarai, Russell R. P.; Kuprov, Ilya; Pervushin, Konstantin

    2010-03-01

    Systematic benchmarking of multi-dimensional protein NMR experiments is a critical prerequisite for optimal allocation of NMR resources for structural analysis of challenging proteins, e.g. large proteins with limited solubility or proteins prone to aggregation. We propose a set of benchmarking parameters for essential protein NMR experiments organized into a lightweight (single XML file) relational database (RDB), which includes all the necessary auxiliaries (waveforms, decoupling sequences, calibration tables, setup algorithms and an RDB management system). The database is interfaced to the Spinach library ( http://spindynamics.org), which enables accurate simulation and benchmarking of NMR experiments on large spin systems. A key feature is the ability to use a single user-specified spin system to simulate the majority of deposited solution state NMR experiments, thus providing the (hitherto unavailable) unified framework for pulse sequence evaluation. This development enables predicting relative sensitivity of deposited implementations of NMR experiments, thus providing a basis for comparison, optimization and, eventually, automation of NMR analysis. The benchmarking is demonstrated with two proteins, of 170 amino acids I domain of αXβ2 Integrin and 440 amino acids NS3 helicase.

  8. Performance Assessment in Fingerprinting and Multi Component Quantitative NMR Analyses.

    PubMed

    Gallo, Vito; Intini, Nicola; Mastrorilli, Piero; Latronico, Mario; Scapicchio, Pasquale; Triggiani, Maurizio; Bevilacqua, Vitoantonio; Fanizzi, Paolo; Acquotti, Domenico; Airoldi, Cristina; Arnesano, Fabio; Assfalg, Michael; Benevelli, Francesca; Bertelli, Davide; Cagliani, Laura R; Casadei, Luca; Cesare Marincola, Flaminia; Colafemmina, Giuseppe; Consonni, Roberto; Cosentino, Cesare; Davalli, Silvia; De Pascali, Sandra A; D'Aiuto, Virginia; Faccini, Andrea; Gobetto, Roberto; Lamanna, Raffaele; Liguori, Francesca; Longobardi, Francesco; Mallamace, Domenico; Mazzei, Pierluigi; Menegazzo, Ileana; Milone, Salvatore; Mucci, Adele; Napoli, Claudia; Pertinhez, Thelma; Rizzuti, Antonino; Rocchigiani, Luca; Schievano, Elisabetta; Sciubba, Fabio; Sobolev, Anatoly; Tenori, Leonardo; Valerio, Mariacristina

    2015-07-01

    An interlaboratory comparison (ILC) was organized with the aim to set up quality control indicators suitable for multicomponent quantitative analysis by nuclear magnetic resonance (NMR) spectroscopy. A total of 36 NMR data sets (corresponding to 1260 NMR spectra) were produced by 30 participants using 34 NMR spectrometers. The calibration line method was chosen for the quantification of a five-component model mixture. Results show that quantitative NMR is a robust quantification tool and that 26 out of 36 data sets resulted in statistically equivalent calibration lines for all considered NMR signals. The performance of each laboratory was assessed by means of a new performance index (named Qp-score) which is related to the difference between the experimental and the consensus values of the slope of the calibration lines. Laboratories endowed with a Qp-score falling within the suitable acceptability range are qualified to produce NMR spectra that can be considered statistically equivalent in terms of relative intensities of the signals. In addition, the specific response of nuclei to the experimental excitation/relaxation conditions was addressed by means of the parameter named NR. NR is related to the difference between the theoretical and the consensus slopes of the calibration lines and is specific for each signal produced by a well-defined set of acquisition parameters. PMID:26020452

  9. Automated protein fold determination using a minimal NMR constraint strategy

    PubMed Central

    Zheng, Deyou; Huang, Yuanpeng J.; Moseley, Hunter N.B.; Xiao, Rong; Aramini, James; Swapna, G.V.T.; Montelione, Gaetano T.

    2003-01-01

    Determination of precise and accurate protein structures by NMR generally requires weeks or even months to acquire and interpret all the necessary NMR data. However, even medium-accuracy fold information can often provide key clues about protein evolution and biochemical function(s). In this article we describe a largely automatic strategy for rapid determination of medium-accuracy protein backbone structures. Our strategy derives from ideas originally introduced by other groups for determining medium-accuracy NMR structures of large proteins using deuterated, 13C-, 15N-enriched protein samples with selective protonation of side-chain methyl groups (13CH3). Data collection includes acquiring NMR spectra for automatically determining assignments of backbone and side-chain 15N, HN resonances, and side-chain 13CH3 methyl resonances. These assignments are determined automatically by the program AutoAssign using backbone triple resonance NMR data, together with Spin System Type Assignment Constraints (STACs) derived from side-chain triple-resonance experiments. The program AutoStructure then derives conformational constraints using these chemical shifts, amide 1H/2H exchange, nuclear Overhauser effect spectroscopy (NOESY), and residual dipolar coupling data. The total time required for collecting such NMR data can potentially be as short as a few days. Here we demonstrate an integrated set of NMR software which can process these NMR spectra, carry out resonance assignments, interpret NOESY data, and generate medium-accuracy structures within a few days. The feasibility of this combined data collection and analysis strategy starting from raw NMR time domain data was illustrated by automatic analysis of a medium accuracy structure of the Z domain of Staphylococcal protein A. PMID:12761394

  10. Quantitative structure parameters from the NMR spectroscopy of quadrupolar nuclei

    DOE PAGESBeta

    Perras, Frédéric A.

    2016-01-01

    Nuclear magnetic resonance (NMR) spectroscopy is one of the most important characterization tools in chemistry, however, 3/4 of the NMR active nuclei are underutilized due to their quadrupolar nature. This short review centers on the development of methods that use solid-state NMR of quadrupolar nuclei for obtaining quantitative structural information. Namely, techniques using dipolar recoupling as well as the resolution afforded by double-rotation are presented for the measurement of spin–spin coupling between quadrupoles, enabling the measurement of internuclear distances and connectivities. Two-dimensional

  11. NMR imaging of components and materials for DOE application

    SciTech Connect

    Richardson, B.R.

    1993-12-01

    The suitability for using NMR imaging to characterize liquid, polymeric, and solid materials was reviewed. The most attractive applications for NMR imaging appear to be liquid-filled porous samples, partially cured polymers, adhesives, and potting compounds, and composite polymers/high explosives containing components with widely varying thermal properties. Solid-state NMR line-narrowing and signal-enhancing markedly improve the imaging possibilities of true solid and materials. These techniques provide unique elemental and chemical shift information for highly complex materials and complement images with similar spatial resolution, such as X-ray computed tomography (CT).

  12. Complete NMR assignments of undegraded asterosaponins from Asterias amurensis.

    PubMed

    Hwang, In Hyun; Kulkarni, Roshan; Yang, Min Hye; Choo, Soo Jin; Zhou, Wei; Lee, Sang Myung; Jang, Tae Su; Jeong, Gil-Saeng; Chang, Hyeun Wook; Na, MinKyun

    2014-10-01

    Four asterosaponins, thornasteroside A (1), versicoside A (2), anasteroside B (3), and asteronylpentaglycoside sulfate (4), were isolated from the predatory starfish Asterias amurensis Lütken. Unlike previous studies focusing on structure elucidation by degradation of the complex saponin molecules, complete nuclear magnetic resonance (NMR) assignment for the intact molecules was accomplished using 600 MHz high magnetic field NMR. The complete set of NMR assignments can help in the structure elucidation of asterosaponins isolated in low yields without resorting to chemical degradation. Furthermore, this approach can be extended to other complex steroidal saponins, which may accelerate the discovery of bioactive secondary metabolites from this invasive starfish species. PMID:24838379

  13. Solid-State NMR Studies of Amyloid Fibril Structure

    NASA Astrophysics Data System (ADS)

    Tycko, Robert

    2011-05-01

    Current interest in amyloid fibrils stems from their involvement in neurodegenerative and other diseases and from their role as an alternative structural state for many peptides and proteins. Solid-state nuclear magnetic resonance (NMR) methods have the unique capability of providing detailed structural constraints for amyloid fibrils, sufficient for the development of full molecular models. In this article, recent progress in the application of solid-state NMR to fibrils associated with Alzheimer's disease, prion fibrils, and related systems is reviewed, along with relevant developments in solid-state NMR techniques and technology.

  14. Nanoscale NMR and NQR with Nitrogen Vacancy Centers

    NASA Astrophysics Data System (ADS)

    Urbach, Elana; Lovchinsky, Igor; Sanchez-Yamagishi, Javier; Choi, Soonwon; Bylinskii, Alexei; Dwyer, Bo; Andersen, Trond; Sushkov, Alex; Park, Hongkun; Lukin, Mikhail

    2016-05-01

    Nuclear quadrupole resonance (NQR) is a powerful tool which is used to detect quadrupolar interaction in nuclear spins with I > 1/2. Conventional NQR and NMR technology, however, rely on measuring magnetic fields from a macroscopic number of spins. Extending NMR and NQR techniques to the nanoscale could allow us to learn structural information about interesting materials and biomolecules. We present recent progress on using Nitrogen-Vacancy (NV) centers in diamond to perform room temperature nanoscale NMR and NQR spectroscopy on small numbers of nuclear spins in hexagonal boron nitride.

  15. NMR studies of metallic tin confined within porous matrices

    SciTech Connect

    Charnaya, E. V.; Tien, Cheng; Lee, M. K.; Kumzerov, Yu. A.

    2007-04-01

    {sup 119}Sn NMR studies were carried out for metallic tin confined within synthetic opal and porous glass. Tin was embedded into nanoporous matrices in the melted state under pressure. The Knight shift for liquid confined tin was found to decrease with decreasing pore size. Correlations between NMR line shapes, Knight shift, and pore filling were observed. The melting and freezing phase transitions of tin under confinement were studied through temperature dependences of NMR signals upon warming and cooling. Melting of tin within the opal matrix agreed well with the liquid skin model suggested for small isolated particles. The influence of the pore filling on the melting process was shown.

  16. Capillary toroid cavity detector for high pressure NMR

    SciTech Connect

    Gerald, II, Rex E.; Chen, Michael J.; Klingler, Robert J.; Rathke, Jerome W.; ter Horst, Marc

    2007-09-11

    A Toroid Cavity Detector (TCD) is provided for implementing nuclear magnetic resonance (NMR) studies of chemical reactions under conditions of high pressures and temperatures. A toroid cavity contains an elongated central conductor extending within the toroid cavity. The toroid cavity and central conductor generate an RF magnetic field for NMR analysis. A flow-through capillary sample container is located within the toroid cavity adjacent to the central conductor to subject a sample material flowing through the capillary to a static magnetic field and to enable NMR spectra to be recorded of the material in the capillary under a temperature and high pressure environment.

  17. Quantitative structure parameters from the NMR spectroscopy of quadrupolar nuclei

    SciTech Connect

    Perras, Frederic A.

    2015-12-15

    Here, nuclear magnetic resonance (NMR) spectroscopy is one of the most important characterization tools in chemistry, however, 3/4 of the NMR active nuclei are underutilized due to their quadrupolar nature. This short review centers on the development of methods that use solid-state NMR of quadrupolar nuclei for obtaining quantitative structural information. Namely, techniques using dipolar recoupling as well as the resolution afforded by double-rotation are presented for the measurement of spin–spin coupling between quadrupoles, enabling the measurement of internuclear distances and connectivities.

  18. New Views of Functionally Dynamic Proteins by Solution NMR Spectroscopy.

    PubMed

    Kay, Lewis E

    2016-01-29

    In the past several decades solution NMR spectroscopy has emerged as a powerful technique for the study of the structure and dynamics of proteins, providing detailed insights into biomolecular function. Herein, I provide a summary of two important areas of application, focusing on NMR studies of (i) supramolecular systems with aggregate molecular masses in the hundreds of kilodaltons and of (ii) sparsely populated and transiently formed protein states that are thermally accessible from populated ground-state conformers. The critical role of molecular dynamics in function is emphasized, highlighting the utility of the NMR technique in providing such often elusive information. PMID:26707200

  19. Structural biology applications of solid state MAS DNP NMR.

    PubMed

    Akbey, Ümit; Oschkinat, Hartmut

    2016-08-01

    Dynamic Nuclear Polarization (DNP) has long been an aim for increasing sensitivity of nuclear magnetic resonance (NMR) spectroscopy, delivering spectra in shorter experiment times or of smaller sample amounts. In recent years, it has been applied in magic angle spinning (MAS) solid-state NMR to a large range of samples, including biological macromolecules and functional materials. New research directions in structural biology can be envisaged by DNP, facilitating investigations on very large complexes or very heterogeneous samples. Here we present a summary of state of the art DNP MAS NMR spectroscopy and its applications to structural biology, discussing the technical challenges and factors affecting DNP performance. PMID:27095695

  20. A simple low-cost single-crystal NMR setup

    NASA Astrophysics Data System (ADS)

    Vinding, Mads S.; Kessler, Tommy O.; Vosegaard, Thomas

    2016-08-01

    A low-cost single-crystal NMR kit is presented along with a web-based post-processing software. The kit consists of a piezo-crystal motor and a goniometer for the crystal, both embedded in a standard wide-bore NMR probe with a 3D printed scaffold. The NMR pulse program controls the angle setting automatically, and the post-processing software incorporates a range of orientation-angle discrepancies present in the kit and other single-crystal setups. Results with a NaNO3 single-crystal show a high degree of reproducibility and excellent agreement with previous findings for the anisotropic quadrupolar interaction.

  1. High-pressure on-line photolysis with NMR detection

    SciTech Connect

    Yonker, C.R.; Wallen, S.L.

    1996-06-01

    The investigation of the photoreversible fulgide Aberchrome-540 as a function of pressure and temperature with the use of nuclear magnetic resonance (NMR) detection is described. This technique demonstrates the novel combination of high-pressure NMR and laser photolysis with the use of fiber optics for the conversion of the fulgide on-line in the instrument. Investigation of the photolysis of Aberchrome-540 to 2.0 kbar and 120 degrees C is reported. Extension of this technique should allow the investigation of photo-initiated reaction kinetics and equilibria as a function of pressure and temperature with simultaneous structural characterization with NMR. {copyright} {ital 1996} {ital Society for Applied Spectroscopy}

  2. NMR studies on polyphosphide Ce6Ni6P17

    NASA Astrophysics Data System (ADS)

    Koyama, T.; Yamada, H.; Ueda, K.; Mito, T.; Aoyama, Y.; Nakano, T.; Takeda, N.

    2016-02-01

    We report the result of 31P nuclear magnetic resonance (NMR) studies on Ce6Ni6P17. The observed NMR spectra show a Lorentzian-type and an asymmetric shapes, reflecting the local symmetry around each P site in the cubic unit cell. We have identified the observed NMR lines corresponding to three inequivalent P sites and deduced the temperature dependence of the Knight shift for each site. The Knight shifts increase with decreasing temperature down to 1.5 K, indicating a localized spin system of Ce6Ni6P17. Antiferromagnetic correlation between 4f spins is suggested from the negative sign of the Weiss-temperature.

  3. Structural biology applications of solid state MAS DNP NMR

    NASA Astrophysics Data System (ADS)

    Akbey, Ümit; Oschkinat, Hartmut

    2016-08-01

    Dynamic Nuclear Polarization (DNP) has long been an aim for increasing sensitivity of nuclear magnetic resonance (NMR) spectroscopy, delivering spectra in shorter experiment times or of smaller sample amounts. In recent years, it has been applied in magic angle spinning (MAS) solid-state NMR to a large range of samples, including biological macromolecules and functional materials. New research directions in structural biology can be envisaged by DNP, facilitating investigations on very large complexes or very heterogeneous samples. Here we present a summary of state of the art DNP MAS NMR spectroscopy and its applications to structural biology, discussing the technical challenges and factors affecting DNP performance.

  4. Analysis of experimentally shocked minerals by NMR spectroscopy

    SciTech Connect

    Cygan, R.T.; Boslough, M.B.

    1994-10-01

    The shock-loading of natural materials by an impact or explosion can result in the formation of modified and altered phases. In order to characterize the resulting material and to evaluate the extent of shock modification, the authors have used nuclear magnetic resonance (NMR) spectroscopy to examine several experimentally shocked minerals. In three related NMR studies, they have (1) examined shocked clinoptilolite, (2) performed a preliminary analysis of shocked quartz, and (3) reproduced shocked quartz results with detailed spectral deconvolutions, and extended it with NMR analysis of shocked feldspar powders.

  5. Solid State NMR Studies of Amyloid Fibril Structure

    PubMed Central

    Tycko, Robert

    2011-01-01

    Current interest in amyloid fibrils stems from their involvement in neurodegenerative and other diseases and from their role as an alternative structural state for many peptides and proteins. Solid state NMR methods have the unique capability of providing detailed structural constraints for amyloid fibrils, sufficient for the development of full molecular models. In this article, recent progress in the application of solid state NMR to fibrils associated with Alzheimer’s disease, prion fibrils, and related systems is reviewed, along with relevant developments in solid state NMR techniques and technology. PMID:21219138

  6. Fragment-Based Drug Discovery Using NMR Spectroscopy

    PubMed Central

    Harner, Mary J.; Frank, Andreas O.; Fesik, Stephen W.

    2013-01-01

    Nuclear magnetic resonance (NMR) spectroscopy has evolved into a powerful tool for fragment-based drug discovery over the last two decades. While NMR has been traditionally used to elucidate the three-dimensional structures and dynamics of biomacromolecules and their interactions, it can also be a very valuable tool for the reliable identification of small molecules that bind to proteins and for hit-to-lead optimization. Here, we describe the use of NMR spectroscopy as a method for fragment-based drug discovery and how to most effectively utilize this approach for discovering novel therapeutics based on our experience. PMID:23686385

  7. NMR Methods, Applications and Trends for Groundwater Evaluation and Management

    NASA Astrophysics Data System (ADS)

    Walsh, D. O.; Grunewald, E. D.

    2011-12-01

    Nuclear magnetic resonance (NMR) measurements have a tremendous potential for improving groundwater characterization, as they provide direct detection and measurement of groundwater and unique information about pore-scale properties. NMR measurements, commonly used in chemistry and medicine, are utilized in geophysical investigations through non-invasive surface NMR (SNMR) or downhole NMR logging measurements. Our recent and ongoing research has focused on improving the performance and interpretation of NMR field measurements for groundwater characterization. Engineering advancements have addressed several key technical challenges associated with SNMR measurements. Susceptibility of SNMR measurements to environmental noise has been dramatically reduced through the development of multi-channel acquisition hardware and noise-cancellation software. Multi-channel instrumentation (up to 12 channels) has also enabled more efficient 2D and 3D imaging. Previous limitations in measuring NMR signals from water in silt, clay and magnetic geology have been addressed by shortening the instrument dead-time from 40 ms to 4 ms, and increasing the power output. Improved pulse sequences have been developed to more accurately estimate NMR relaxation times and their distributions, which are sensitive to pore size distributions. Cumulatively, these advancements have vastly expanded the range of environments in which SNMR measurements can be obtained, enabling detection of groundwater in smaller pores, in magnetic geology, in the unsaturated zone, and nearby to infrastructure (presented here in case studies). NMR logging can provide high-resolution estimates of bound and mobile water content and pore size distributions. While NMR logging has been utilized in oil and gas applications for decades, its use in groundwater investigations has been limited by the large size and high cost of oilfield NMR logging tools and services. Recently, engineering efforts funded by the US Department of

  8. Jointly deriving NMR surface relaxivity and pore size distributions by NMR relaxation experiments on partially desaturated rocks

    NASA Astrophysics Data System (ADS)

    Mohnke, O.; Hughes, B.

    2014-06-01

    Nuclear magnetic resonance (NMR) relaxometry is a geophysical method widely used in borehole and laboratory applications to nondestructively infer transport and storage properties of rocks and soils as it is directly sensitive to the water/oil content and pore sizes. However, for inferring pore sizes, NMR relaxometry data need to be calibrated with respect to a surface interaction parameter, surface relaxivity, which depends on the type and mineral constituents of the investigated rock. This study introduces an inexpensive and quick alternative to the classical calibration methods, e.g., mercury injection, pulsed field gradient (PFG) NMR, or grain size analysis, which allows for jointly estimating NMR surface relaxivity and pore size distributions using NMR relaxometry data from partially desaturated rocks. Hereby, NMR relaxation experiments are performed on the fully saturated sample and on a sample partially drained at a known differential pressure. Based on these data, the (capillary) pore radius distribution and surface relaxivity are derived by joint optimization of the Brownstein-Tarr and the Young-Laplace equation assuming parallel capillaries. Moreover, the resulting pore size distributions can be used to predict water retention curves. This inverse modeling approach—tested and validated using NMR relaxometry data measured on synthetic porous borosilicate samples with known petrophysical properties (i.e., permeability, porosity, inner surfaces, pore size distributions)—yields consistent and reproducible estimates of surface relaxivity and pore radii distributions. Also, subsequently calculated water retention curves generally correlate well with measured water retention curves.

  9. Biodegradation pathway of mesotrione: complementarities of NMR, LC-NMR and LC-MS for qualitative and quantitative metabolic profiling.

    PubMed

    Durand, Stéphanie; Sancelme, Martine; Besse-Hoggan, Pascale; Combourieu, Bruno

    2010-09-01

    Enhanced knowledge of pesticide transformation products formed in the environment could lead to both accurate estimates of the overall effects of these compounds on environmental ecosystems and human health and improved removal processes. These compounds can present chemical and environmental behaviours completely different from the starting active ingredient. The difficulty lies on their identification or/and their quantification due to the lack of analytical reference standards. In this context, ex situ Nuclear Magnetic Resonance (NMR) and Liquid Chromatography-NMR (LC-NMR) were used as complementary tools to LC-Mass Spectrometry (MS) to define the metabolic pathway of mesotrione, an emergent herbicide, by the bacterial strain Bacillus sp. 3B6. The complementarities of ex situ and LC-NMR allowed us to unambiguously identify six metabolites whereas the structures of only four metabolites were suggested by LC-MS. The presence of a new metabolic pathway was evidenced by NMR. These results demonstrate that NMR and LC-NMR spectroscopy provided unambiguous structural information for xenobiotic metabolic profiling, even at moderate magnetic field and allowed direct absolute quantification despite the lack of commercial or synthetic standards, required for LC-MS techniques. PMID:20692682

  10. NMR Spectroscopy for Thin Films by Magnetic Resonance Force Microscopy

    PubMed Central

    Won, Soonho; Saun, Seung-Bo; Lee, Soonchil; Lee, SangGap; Kim, Kiwoong; Han, Yunseok

    2013-01-01

    Nuclear magnetic resonance (NMR) is a fundamental research tool that is widely used in many fields. Despite its powerful applications, unfortunately the low sensitivity of conventional NMR makes it difficult to study thin film or nano-sized samples. In this work, we report the first NMR spectrum obtained from general thin films by using magnetic resonance force microscopy (MRFM). To minimize the amount of imaging information inevitably mixed into the signal when a gradient field is used, we adopted a large magnet with a flat end with a diameter of 336 μm that generates a homogeneous field on the sample plane and a field gradient in a direction perpendicular to the plane. Cyclic adiabatic inversion was used in conjunction with periodic phase inversion of the frequency shift to maximize the SNR. In this way, we obtained the 19F NMR spectrum for a 34 nm-thick CaF2 thin film. PMID:24217000

  11. International NMR-based Environmental Metabolomics Intercomparison Exercise

    EPA Science Inventory

    Several fundamental requirements must be met so that NMR-based metabolomics and the related technique of metabonomics can be formally adopted into environmental monitoring and chemical risk assessment. Here we report an intercomparison exercise which has evaluated the effectivene...

  12. Structural Biology by NMR: Structure, Dynamics, and Interactions

    PubMed Central

    Markwick, Phineus R. L.; Malliavin, Thérèse; Nilges, Michael

    2008-01-01

    The function of bio-macromolecules is determined by both their 3D structure and conformational dynamics. These molecules are inherently flexible systems displaying a broad range of dynamics on time-scales from picoseconds to seconds. Nuclear Magnetic Resonance (NMR) spectroscopy has emerged as the method of choice for studying both protein structure and dynamics in solution. Typically, NMR experiments are sensitive both to structural features and to dynamics, and hence the measured data contain information on both. Despite major progress in both experimental approaches and computational methods, obtaining a consistent view of structure and dynamics from experimental NMR data remains a challenge. Molecular dynamics simulations have emerged as an indispensable tool in the analysis of NMR data. PMID:18818721

  13. Mixing and Matching Detergents for Membrane Protein NMR Structure Determination

    SciTech Connect

    Columbus, Linda; Lipfert, Jan; Jambunathan, Kalyani; Fox, Daniel A.; Sim, Adelene Y.L.; Doniach, Sebastian; Lesley, Scott A.

    2009-10-21

    One major obstacle to membrane protein structure determination is the selection of a detergent micelle that mimics the native lipid bilayer. Currently, detergents are selected by exhaustive screening because the effects of protein-detergent interactions on protein structure are poorly understood. In this study, the structure and dynamics of an integral membrane protein in different detergents is investigated by nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) spectroscopy and small-angle X-ray scattering (SAXS). The results suggest that matching of the micelle dimensions to the protein's hydrophobic surface avoids exchange processes that reduce the completeness of the NMR observations. Based on these dimensions, several mixed micelles were designed that improved the completeness of NMR observations. These findings provide a basis for the rational design of mixed micelles that may advance membrane protein structure determination by NMR.

  14. Applications of high resolution /sup 3/H NMR spectroscopy

    SciTech Connect

    Williams, P.G.

    1987-10-01

    The advantages of tritium as an NMR nucleus are pointed out. Examples of its use are given, including labelled toluene, hydrogenation of ..beta..-methylstyrene, and maltose and its binding proteins. 7 refs., 2 figs. (DLC)

  15. Multiplet-separated heteronuclear two-dimensional NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Levitt, Malcolm H.; Sørensen, O. W.; Ernst, R. R.

    1983-02-01

    Techniques are described for the identification and separation of peaks of different multiplicity in heteronuclear two-dimensional NMR spectroscopy. The methods are applied to the two-dimensional 13C- 1H shift correlation spectrum of menthol.

  16. A Demonstration of Imaging on an NMR Spectrometer.

    ERIC Educational Resources Information Center

    Hull, L. A.

    1990-01-01

    Described is a simple demonstration that relates the techniques of magnetic resonance imaging (MRI) used in medicine and nuclear magnetic resonance (NMR) spectroscopy. Included are materials, procedures, and probable results. (KR)

  17. Proton NMR Spectra: Deceptively Simple and Deceptively Complex Examples.

    ERIC Educational Resources Information Center

    Gurst, J. E.; And Others

    1985-01-01

    Describes relatively simple nuclear magnetic resonance (NMR) experiments that demonstrate unexpected results of the deceptively simple and deceptively complex types. Background information, experimental procedures, and typical results obtained are included. (JN)

  18. Revisiting Protocols for the NMR Analysis of Bacterial Metabolomes

    PubMed Central

    Halouska, Steven; Zhang, Bo; Gaupp, Rosmarie; Lei, Shulei; Snell, Emily; Fenton, Robert J.; Barletta, Raul G.; Somerville, Greg A.; Powers, Robert

    2015-01-01

    Over the past decade, metabolomics has emerged as an important technique for systems biology. Measuring all the metabolites in a biological system provides an invaluable source of information to explore various cellular processes, and to investigate the impact of environmental factors and genetic modifications. Nuclear magnetic resonance (NMR) spectroscopy is an important method routinely employed in metabolomics. NMR provides comprehensive structural and quantitative information useful for metabolomics fingerprinting, chemometric analysis, metabolite identification and metabolic pathway construction. A successful metabolomics study relies on proper experimental protocols for the collection, handling, processing and analysis of metabolomics data. Critically, these protocols should eliminate or avoid biologically-irrelevant changes to the metabolome. We provide a comprehensive description of our NMR-based metabolomics procedures optimized for the analysis of bacterial metabolomes. The technical details described within this manuscript should provide a useful guide to reliably apply our NMR-based metabolomics methodology to systems biology studies. PMID:26078915

  19. A 19F NMR Study of Enzyme Activity

    NASA Astrophysics Data System (ADS)

    Peterman, Keith E.; Lentz, Kevin; Duncan, Jeffery

    1998-10-01

    This basic enzyme activity laboratory experiment demonstrates how 19F NMR can be used in biochemical studies and presents the advantages of 19F NMR over 1H NMR for studies of this nature. N-Trifluoroacetylglycine was selected as a commercially available model fluorine-tagged substrate that readily undergoes acylase I-catalyzed hydrolysis to produce trifluoroacetic acid and glycine. Progress of the reaction was monitored by following conversion of the trifluoroacetyl moiety peak of N-trifluoroacetylglycine to trifluoroacetic acid. The extent of hydrolysis was determined by comparing integrated ratios of the two 19F NMR peaks. A plot of percent hydrolysis versus enzyme concentration was used to calculate unit activity of the enzyme. This is a viable laboratory experiment for junior/senior-level courses in instrumental analytical chemistry, biochemistry, molecular biology, or spectroscopy.

  20. NMR study of some coumarins and furocoumarins methylated

    NASA Astrophysics Data System (ADS)

    Miranda, R.; Santana, L.; Uriarte, E.; Zagotto, G.

    1994-01-01

    The 1H and 13C NMR spectra of various methylcoumarins and methylfurocoumarins are reported. All signals were assigned and the influence on chemical shifts of methylation at various positions was determined.

  1. Prediction of Bioactive Compounds Using Computed NMR Chemical Shifts.

    PubMed

    Karthikeyan, Muthukumarasamy; Rajamohanan, Pattuparambil Ramanpillai; Vyas, Renu

    2015-01-01

    NMR based chemical shifts are an important diagnostic parameter for structure elucidation as they capture rich information related to conformational, electronic and stereochemical arrangement of functional groups in a molecule which is responsible for its activity towards any biological target. The present work discusses the importance of computing NMR chemical shifts from molecular structures. The NMR chemical shift data (experimental or computed) was used to generate fingerprints in binary formats for mapping molecular fragments (as descriptors) and correlating with the bioactivity classes. For this study, chemical shift data derived binary fingerprints were computed for 149 classes and 4800 bioactive molecules. The sensitivity and selectivity of fingerprints in discriminating molecules belonging to different therapeutic categories was assessed using a LibSVM based classifier. An accuracy of 82% for proton and 94% for carbon NMR fingerprints were obtained for anti-psoriatic and anti-psychotic molecules demonstrating the effectiveness of this approach for virtual screening. PMID:26138568

  2. Study of molecular interactions with 13C DNP-NMR

    NASA Astrophysics Data System (ADS)

    Lerche, Mathilde H.; Meier, Sebastian; Jensen, Pernille R.; Baumann, Herbert; Petersen, Bent O.; Karlsson, Magnus; Duus, Jens Ø.; Ardenkjær-Larsen, Jan H.

    2010-03-01

    NMR spectroscopy is an established, versatile technique for the detection of molecular interactions, even when these interactions are weak. Signal enhancement by several orders of magnitude through dynamic nuclear polarization alleviates several practical limitations of NMR-based interaction studies. This enhanced non-equilibrium polarization contributes sensitivity for the detection of molecular interactions in a single NMR transient. We show that direct 13C NMR ligand binding studies at natural isotopic abundance of 13C gets feasible in this way. Resultant screens are easy to interpret and can be performed at 13C concentrations below μM. In addition to such ligand-detected studies of molecular interaction, ligand binding can be assessed and quantified with enzymatic assays that employ hyperpolarized substrates at varying enzyme inhibitor concentrations. The physical labeling of nuclear spins by hyperpolarization thus provides the opportunity to devise fast novel in vitro experiments with low material requirement and without the need for synthetic modifications of target or ligands.

  3. A Short Set of Carbon 13-NMR Correlation Tables.

    ERIC Educational Resources Information Center

    Brown, D. W.

    1985-01-01

    Presents a short set of carbon-13 nuclear magnetic resonance (NMR) tables. These tables not only serve pedagogic purposes but also allow students to do calculations rapidly and with acceptable accuracy for a wide variety of compounds. (JN)

  4. A Covariance NMR Toolbox for MATLAB and OCTAVE

    NASA Astrophysics Data System (ADS)

    Short, Timothy; Alzapiedi, Leigh; Brüschweiler, Rafael; Snyder, David

    2011-03-01

    The Covariance NMR Toolbox is a new software suite that provides a streamlined implementation of covariance-based analysis of multi-dimensional NMR data. The Covariance NMR Toolbox uses the MATLAB or, alternatively, the freely available GNU OCTAVE computer language, providing a user-friendly environment in which to apply and explore covariance techniques. Covariance methods implemented in the toolbox described here include direct and indirect covariance processing, 4D covariance, generalized indirect covariance (GIC), and Z-matrix transform. In order to provide compatibility with a wide variety of spectrometer and spectral analysis platforms, the Covariance NMR Toolbox uses the NMRPipe format for both input and output files. Additionally, datasets small enough to fit in memory are stored as arrays that can be displayed and further manipulated in a versatile manner within MATLAB or OCTAVE.

  5. A covariance NMR toolbox for MATLAB and OCTAVE.

    PubMed

    Short, Timothy; Alzapiedi, Leigh; Brüschweiler, Rafael; Snyder, David

    2011-03-01

    The Covariance NMR Toolbox is a new software suite that provides a streamlined implementation of covariance-based analysis of multi-dimensional NMR data. The Covariance NMR Toolbox uses the MATLAB or, alternatively, the freely available GNU OCTAVE computer language, providing a user-friendly environment in which to apply and explore covariance techniques. Covariance methods implemented in the toolbox described here include direct and indirect covariance processing, 4D covariance, generalized indirect covariance (GIC), and Z-matrix transform. In order to provide compatibility with a wide variety of spectrometer and spectral analysis platforms, the Covariance NMR Toolbox uses the NMRPipe format for both input and output files. Additionally, datasets small enough to fit in memory are stored as arrays that can be displayed and further manipulated in a versatile manner within MATLAB or OCTAVE. PMID:21215669

  6. Cell signaling, post-translational protein modifications and NMR spectroscopy

    PubMed Central

    Theillet, Francois-Xavier; Smet-Nocca, Caroline; Liokatis, Stamatios; Thongwichian, Rossukon; Kosten, Jonas; Yoon, Mi-Kyung; Kriwacki, Richard W.; Landrieu, Isabelle; Lippens, Guy

    2016-01-01

    Post-translationally modified proteins make up the majority of the proteome and establish, to a large part, the impressive level of functional diversity in higher, multi-cellular organisms. Most eukaryotic post-translational protein modifications (PTMs) denote reversible, covalent additions of small chemical entities such as phosphate-, acyl-, alkyl- and glycosyl-groups onto selected subsets of modifiable amino acids. In turn, these modifications induce highly specific changes in the chemical environments of individual protein residues, which are readily detected by high-resolution NMR spectroscopy. In the following, we provide a concise compendium of NMR characteristics of the main types of eukaryotic PTMs: serine, threonine, tyrosine and histidine phosphorylation, lysine acetylation, lysine and arginine methylation, and serine, threonine O-glycosylation. We further delineate the previously uncharacterized NMR properties of lysine propionylation, butyrylation, succinylation, malonylation and crotonylation, which, altogether, define an initial reference frame for comprehensive PTM studies by high-resolution NMR spectroscopy. PMID:23011410

  7. A statistical analysis of NMR spectrometer noise.

    PubMed

    Grage, Halfdan; Akke, Mikael

    2003-05-01

    Estimation of NMR spectral parameters, using e.g. maximum likelihood methods, is commonly based on the assumption of white complex Gaussian noise in the signal obtained by quadrature detection. Here we present a statistical analysis with the purpose of discussing and testing the validity of this fundamental assumption. Theoretical expressions are derived for the correlation structure of the noise under various conditions, showing that in general the noise in the sampled signal is not strictly white, even if the thermal noise in the receiver steps prior to digitisation can be characterised as white Gaussian noise. It is shown that the noise correlation properties depend on the ratio between the sampling frequency and the filter cut-off frequency, as well as the filter characteristics. The theoretical analysis identifies conditions that are expected to yield non-white noise in the sampled signal. Extensive statistical characterisation of experimental noise confirms the theoretical predictions. The statistical methods outlined here are also useful for residual analysis in connection with validation of the model and the parameter estimates. PMID:12762994

  8. NMR Studies of Enzyme Structure and Mechanism

    NASA Astrophysics Data System (ADS)

    Mildvan, Albert

    2006-03-01

    At least three NMR methodologies pioneered by Al Redfield, have greatly benefited enzymology: (1) the suppression of strong water signals without pre-saturation; (2) sequence specific NH/ND exchange; and (3) dynamic studies of mobile loops of proteins. Water suppression has enabled us to identify unusually short, strong H-bonds at the active sites of five enzymes (three isomerases and two esterases), and to measure their lengths from both the chemical shifts and D/H fractionation factors of the deshielded protons involved (J. Mol. Struct. 615, 163 (2002)). Backbone NH exchange studies were used to detect regions of an NTP pyrophosphohydrolase in which NH groups became selectively protected against exchange on Mg(2+) binding, and further protected on product (NMP) binding, thus locating binding sites as well as conformationally linked remote sites (Biochemistry 42, 10140 (2003)). Dynamic studies were used to elucidate the frequency of motion of a flexible loop of GDP-mannose hydrolase (66,000/sec) containing the catalytic base His-124, from exchange broadening of the side chain NH signals of His-124 in the free enzyme. The binding of Mg(2+) and GDP-mannose lock His-124 in position to deprotonate the entering water and complete the reaction.

  9. NMR velocity imaging of single liquid drops

    NASA Astrophysics Data System (ADS)

    Amar, A.; Stapf, S.; Bluemich, B.

    2007-03-01

    Liquid-liquid extraction processes are often found in industrial applications when a bulk phase needs to be purified from dissolved components. The extraction strategy consists of dissolving the impurities into a second, carrier phase, with optimal performance being guaranteed by maximizing both contact interface area and mass transfer rate, in the shape of a swarm of dispersed droplets. Their buoyancy-driven flow within the continuous medium induces internal fluid motion driven by momentum transfer at the drop surface. This convective transport enhances mass transfer and the efficiency of an extraction column. However, understanding mass transfer depends on a proper description of the flow field inside and outside the drops. For that purpose, a cell was built that enables the levitation of a single drop within a counterstream of water. NMR velocity imaging was then applied to drops of different fluids to monitor the internal dynamics as a function of drop size, age, and interface tension. Vortex-type patterns in at least part of the drop were observed where their size and velocity magnitude depended on the system impurity concentration.

  10. A multinuclear static NMR study of geopolymerisation

    SciTech Connect

    Favier, Aurélie; Habert, Guillaume; Roussel, Nicolas; D'Espinose de Lacaillerie, Jean-Baptiste

    2015-09-15

    Geopolymers are inorganic binders obtained by alkali activation of aluminosilicates. While the structure of geopolymers is now well understood, the details of the geopolymerisation reaction and their impact on the rheology of the paste remain uncertain. In this work, we follow the elastic properties of a paste made with metakaolin and sodium silicate solution. After the first sharp increase of elastic modulus occurring a few hundred of seconds after mixing and related to the heterogeneous formation of an alumina–silicate gel with a molar ratio Si/Al < 4 located at the grains boundaries, we focus on the progressive increase in elastic modulus on a period of few hours during the setting of the geopolymer. In this study, we combine the study of rheological properties of the paste with {sup 23}Na, {sup 27}Al and {sup 29}Si static NMR measurement in order to better understand the origin of this second increase in elastic modulus. Our results show that, after a few hours, Al and Na evolution in the liquid phase are concomitant. This suggests the precipitation of an aluminosilicate phase where Al is in tetrahedral position and Na compensates the charge. Furthermore, Si speciation confirms this result and allows us to identify the precipitation of a product, which has a chemical composition close to the final composition of geopolymer. This study provides strong evidence for a heterogeneous formation of an aluminosilicate glass directly from the first gel and the silicate solution without the need for a reorganisation of Gel 1 into Gel 2.

  11. Para-hydrogen perspectives in hyperpolarized NMR.

    PubMed

    Glöggler, Stefan; Colell, Johannes; Appelt, Stephan

    2013-10-01

    The first instance of para-hydrogen induced polarization (PHIP) in an NMR experiment was serendipitously observed in the 1980s while investigating a hydrogenation reaction (Seldler et al., 1983; Bowers and Weitekamp, 1986, 1987; Eisenschmid et al., 1987) [1-4]. Remarkably a theoretical investigation of the applicability of para-hydrogen as a hyperpolarization agent was being performed in the 1980's thereby quickly providing a theoretical basis for the PHIP-effect (Bowers and Weitekamp, 1986) [2]. The discovery of signal amplification by a non-hydrogenating interaction with para-hydrogen has recently extended the interest to exploit the PHIP effect, as it enables investigation of compounds without structural alteration while retaining the advantages of spectroscopy with hyperpolarized compounds [5]. In this article we will place more emphasis of the future applications of the method while only briefly discussing the efforts that have been made in the understanding of the phenomenon and the development of the method so far. PMID:23932399

  12. Silver-109 NMR spectroscopy of inorganic solids.

    PubMed

    Penner, Glenn H; Li, Wenli

    2004-09-01

    In this study the (109)Ag NMR spectra of the following solid inorganic silver-containing compounds were investigated: AgNO(3), AgNO(2), Ag(2)SO(4), Ag(2)SO(3), AgCO(3), Ag(3)PO(4), AgCl, AgBr, AgI, AgSO(3)CH(3), silver p-toluenesulfonate, NaAg(CN)(2), KAg(CN)(2), K(3)Ag(CN)(4), Me(4)NAgCl(2), silver diethylthiocarbamate, silver lactate, silver acetate, silver citrate, and bis[(N,N(1)-di-tert-butylformamidinato)silver(I)]. The magic angle spinning (MAS) spectra of all compounds were obtained. In some cases, when protons were available, the (1)H to (109)Ag cross-polarization (CP) technique was used to enhance the signal and shorten the experimental relaxation delay. It was possible to obtain slow MAS (or CP/MAS) or nonspinning spectra for 10 samples, allowing the determination of the principal components of the (109)Ag chemical shift (CS) tensors. The isotropic chemical shifts and the CS tensors are discussed in light of the available crystal structures. The need for an accepted standard for referencing (109)Ag chemical shifts and the use of AgSO(3)CH(3) as a CP setup sample are also discussed. PMID:15332810

  13. Improvements in Technique of NMR Imaging and NMR Diffusion Measurements in the Presence of Background Gradients.

    NASA Astrophysics Data System (ADS)

    Lian, Jianyu

    In this work, modification of the cosine current distribution rf coil, PCOS, has been introduced and tested. The coil produces a very homogeneous rf magnetic field, and it is inexpensive to build and easy to tune for multiple resonance frequency. The geometrical parameters of the coil are optimized to produce the most homogeneous rf field over a large volume. To avoid rf field distortion when the coil length is comparable to a quarter wavelength, a parallel PCOS coil is proposed and discussed. For testing rf coils and correcting B _1 in NMR experiments, a simple, rugged and accurate NMR rf field mapping technique has been developed. The method has been tested and used in 1D, 2D, 3D and in vivo rf mapping experiments. The method has been proven to be very useful in the design of rf coils. To preserve the linear relation between rf output applied on an rf coil and modulating input for an rf modulating -amplifying system of NMR imaging spectrometer, a quadrature feedback loop is employed in an rf modulator with two orthogonal rf channels to correct the amplitude and phase non-linearities caused by the rf components in the rf system. The modulator is very linear over a large range and it can generate an arbitrary rf shape. A diffusion imaging sequence has been developed for measuring and imaging diffusion in the presence of background gradients. Cross terms between the diffusion sensitizing gradients and background gradients or imaging gradients can complicate diffusion measurement and make the interpretation of NMR diffusion data ambiguous, but these have been eliminated in this method. Further, the background gradients has been measured and imaged. A dipole random distribution model has been established to study background magnetic fields Delta B and background magnetic gradients G_0 produced by small particles in a sample when it is in a B_0 field. From this model, the minimum distance that a spin can approach a particle can be determined by measuring

  14. Quantitative NMR Analysis of Partially Substituted Biodiesel Glycerols

    SciTech Connect

    Nagy, M.; Alleman, T. L.; Dyer, T.; Ragauskas, A. J.

    2009-01-01

    Phosphitylation of hydroxyl groups in biodiesel samples with 2-chloro-4,4,5,5-tetramethyl-1,3,2-dioxaphospholane followed by 31P-NMR analysis provides a rapid quantitative analytical technique for the determination of substitution patterns on partially esterified glycerols. The unique 31P-NMR chemical shift data was established with a series mono and di-substituted fatty acid esters of glycerol and then utilized to characterize an industrial sample of partially processed biodiesel.

  15. Development and application of proton NMR methodology to lipoprotein analysis

    NASA Astrophysics Data System (ADS)

    Korhonen, Ari Juhani

    1998-11-01

    The present thesis describes the development of 1H NMR spectroscopy and its applications to lipoprotein analysis in vitro, utilizing biochemical prior knowledge and advanced lineshape fitting analysis in the frequency domain. A method for absolute quantification of lipoprotein lipids and proteins directly from the terminal methyl-CH3 resonance region of 1H NMR spectra of human blood plasma is described. Then the use of NMR methodology in time course studies of the oxidation process of LDL particles is presented. The function of the cholesteryl ester transfer protein (CETP) in lipoprotein mixtures was also assessed by 1H NMR, which allows for dynamic follow-up of the lipid transfer reactions between VLDL, LDL, and HDL particles. The results corroborated the suggestion that neutral lipid mass transfer among lipoproteins is not an equimolar heteroexchange. A novel method for studying lipoprotein particle fusion is also demonstrated. It is shown that the progression of proteolytically (α- chymotrypsin) induced fusion of LDL particles can be followed by 1H NMR spectroscopy and, moreover, that fusion can be distinguished from aggregation. In addition, NMR methodology was used to study the changes in HDL3 particles induced by phospholipid transfer protein (PLTP) in HDL3 + PLTP mixtures. The 1H NMR study revealed a gradual production of enlarged HDL particles, which demonstrated that PLTP-mediated remodeling of HDL involves fusion of the HDL particles. These applications demonstrated that the 1H NMR approach offers several advantages both in quantification and in time course studies of lipoprotein-lipoprotein interactions and of enzyme/lipid transfer protein function.

  16. NMR Quantitation of Natural Products at the Nanomole-Scale

    PubMed Central

    Dalisay, Doralyn S.; Molinski, Tadeusz F.

    2009-01-01

    We describe a simple and accurate method for quantitation by solvent 13C-satellites (QSCS), of very small amounts of natural products using microprobe NMR spectroscopy. The method takes advantage of integration of 13C satellite peaks of deuterated solvents, in particular CDCl3, that have favorable intensities for measurements of samples in NMR microcoils and microprobe tubes in the 1–200 nanomole range. PMID:19399996

  17. Flow units from integrated WFT and NMR data

    SciTech Connect

    Kasap, E.; Altunbay, M.; Georgi, D.

    1997-08-01

    Reliable and continuous permeability profiles are vital as both hard and soft data required for delineating reservoir architecture. They can improve the vertical resolution of seismic data, well-to-well stratigraphic correlations, and kriging between the well locations. In conditional simulations, permeability profiles are imposed as the conditioning data. Variograms, covariance functions and other geostatistical indicators are more reliable when based on good quality permeability data. Nuclear Magnetic Resonance (NMR) logging and Wireline Formation Tests (WFT) separately generate a wealth of information, and their synthesis extends the value of this information further by providing continuous and accurate permeability profiles without increasing the cost. NMR and WFT data present a unique combination because WFTs provide discrete, in situ permeability based on fluid-flow, whilst NMR responds to the fluids in the pore space and yields effective porosity, pore-size distribution, bound and moveable fluid saturations, and permeability. The NMR permeability is derived from the T{sub 2}-distribution data. Several equations have been proposed to transform T{sub 2} data to permeability. Regardless of the transform model used, the NMR-derived permeabilities depend on interpretation parameters that may be rock specific. The objective of this study is to integrate WFT permeabilities with NMR-derived, T{sub 2} distribution-based permeabilities and thereby arrive at core quality, continuously measured permeability profiles. We outlined the procedures to integrate NMR and WFT data and applied the procedure to a field case. Finally, this study advocates the use of hydraulic unit concepts to extend the WFT-NMR derived, core quality permeabilities to uncored intervals or uncored wells.

  18. Rapid characterization of molecular diffusion by NMR spectroscopy.

    PubMed

    Pudakalakatti, Shivanand M; Chandra, Kousik; Thirupathi, Ravula; Atreya, Hanudatta S

    2014-11-24

    An NMR-based approach for rapid characterization of translational diffusion of molecules has been developed. Unlike the conventional method of acquiring a series of 2D (13)C and (1)H spectra, the proposed approach involves a single 2D NMR spectrum, which can be acquired in minutes. Using this method, it was possible to detect the presence of intermediate oligomeric species of diphenylalanine in solution during the process of its self-assembly to form nanotubular structures. PMID:25331210

  19. Deuterium incorporation in biomass cell wall components by NMR analysis

    SciTech Connect

    Foston, Marcus B; McGaughey, Joseph; O'Neill, Hugh Michael; Evans, Barbara R; Ragauskas, Arthur J

    2012-01-01

    A commercially available deuterated kale sample was analyzed for deuterium incorporation by ionic liquid solution 2H and 1H nuclear magnetic resonance (NMR). This protocol was found to effectively measure the percent deuterium incorporation at 33%, comparable to the 31% value determined by combustion. The solution NMR technique also suggested by a qualitative analysis that deuterium is preferentially incorporated into the carbohydrate components of the kale sample.

  20. Pore structure characterization of catalyst supports via low field NMR

    SciTech Connect

    Smith, D.M.; Glaves, C.L.; Gallegos, D.P.; Brinker, C.J.

    1988-01-01

    In this paper, the application of low-field NMR to both surface area and pore structure analysis of catalyst supports will be presented. Low-field (20 MHz) spin-lattice relaxation (T/sub 1/) experiments are performed on fluids contained in alumina and silica catalyst supports. Pore size distributions (PSD) calculated from these NMR experiments are compared to those obtained from mercury porosimetry and nitrogen condensation. 18 refs., 4 figs., 2 tabs.

  1. Chemical shift referencing in MAS solid state NMR

    NASA Astrophysics Data System (ADS)

    Morcombe, Corey R.; Zilm, Kurt W.

    2003-06-01

    Solid state 13C magic angle spinning (MAS) NMR spectra are typically referenced externally using a probe which does not incorporate a field frequency lock. Solution NMR shifts on the other hand are more often determined with respect to an internal reference and using a deuterium based field frequency lock. Further differences arise in solution NMR of proteins and nucleic acids where both 13C and 1H shifts are referenced by recording the frequency of the 1H resonance of DSS (sodium salt of 2,2-dimethyl-2-silapentane-5-sulphonic acid) instead of TMS (tetramethylsilane). In this note we investigate the difficulties in relating shifts measured relative to TMS and DSS by these various approaches in solution and solids NMR, and calibrate adamantane as an external 13C standard for solids NMR. We find that external chemical shift referencing of magic angle spinning spectra is typically quite reproducible and accurate, with better than ±0.03 ppm accuracy being straight forward to achieve. Solid state and liquid phase NMR shifts obtained by magic angle spinning with external referencing agree with those measured using typical solution NMR hardware with the sample tube aligned with the applied field as long as magnetic susceptibility corrections and solvent shifts are taken into account. The DSS and TMS reference scales for 13C and 1H are related accurately using MAS NMR. Large solvent shifts for the 13C resonance in TMS in either deuterochloroform or methanol are observed, being +0.71 ppm and -0.74 ppm from external TMS, respectively. The ratio of the 13C resonance frequencies for the two carbons in solid adamantane to the 1H resonance of TMS is reported.

  2. Chemical shift referencing in MAS solid state NMR.

    PubMed

    Morcombe, Corey R; Zilm, Kurt W

    2003-06-01

    Solid state 13C magic angle spinning (MAS) NMR spectra are typically referenced externally using a probe which does not incorporate a field frequency lock. Solution NMR shifts on the other hand are more often determined with respect to an internal reference and using a deuterium based field frequency lock. Further differences arise in solution NMR of proteins and nucleic acids where both 13C and 1H shifts are referenced by recording the frequency of the 1H resonance of DSS (sodium salt of 2,2-dimethyl-2-silapentane-5-sulphonic acid) instead of TMS (tetramethylsilane). In this note we investigate the difficulties in relating shifts measured relative to TMS and DSS by these various approaches in solution and solids NMR, and calibrate adamantane as an external 13C standard for solids NMR. We find that external chemical shift referencing of magic angle spinning spectra is typically quite reproducible and accurate, with better than +/-0.03 ppm accuracy being straight forward to achieve. Solid state and liquid phase NMR shifts obtained by magic angle spinning with external referencing agree with those measured using typical solution NMR hardware with the sample tube aligned with the applied field as long as magnetic susceptibility corrections and solvent shifts are taken into account. The DSS and TMS reference scales for 13C and 1H are related accurately using MAS NMR. Large solvent shifts for the 13C resonance in TMS in either deuterochloroform or methanol are observed, being +0.71 ppm and -0.74 ppm from external TMS, respectively. The ratio of the 13C resonance frequencies for the two carbons in solid adamantane to the 1H resonance of TMS is reported. PMID:12810033

  3. Fluid-Rock Characterization and Interactions in NMR Well Logging

    SciTech Connect

    Hirasaki, George J.; Mohanty, Kishore K.

    2003-02-10

    The objective of this project was to characterize the fluid properties and fluid-rock interactions which are needed for formation evaluation by NMR well logging. NMR well logging is finding wide use in formation evaluation. The formation parameters commonly estimated were porosity, permeability, and capillary bound water. Special cases include estimation of oil viscosity, residual oil saturation, location of oil/water contact, and interpretation on whether the hydrocarbon is oil or gas.

  4. Laundering and Deinking Applications of 1H NMR Imaging

    NASA Astrophysics Data System (ADS)

    Tutunjian, P. N.; Borchardt, J. K.; Prieto, N. E.; Raney, K. H.; Ferris, J. A.

    One-dimensional 1H NMR imaging techniques are used to visualize oil removal from fabrics and paper fibers immersed in aqueous solutions of nonionic detergents. The method provides a unique approach to the study of oil-removal kinetics in nonionic detergent systems where traditional optical techniques fail due to solution turbidity. The only requirement of the NMR experiment is the use of deuterated water in order to selectively image the hydrocarbon phase. Preliminary applications to laundering and paper deinking are discussed.

  5. Reaction monitoring using online vs tube NMR spectroscopy: seriously different results.

    PubMed

    Foley, David A; Dunn, Anna L; Zell, Mark T

    2016-06-01

    We report findings from the qualitative evaluation of nuclear magnetic resonance (NMR) reaction monitoring techniques of how each relates to the kinetic profile of a reaction process. The study highlights key reaction rate differences observed between the various NMR reaction monitoring methods investigated: online NMR, static NMR tubes, and periodic inversion of NMR tubes. The analysis of three reaction processes reveals that rates derived from NMR analysis are highly dependent on monitoring method. These findings indicate that users must be aware of the effect of their monitoring method upon the kinetic rate data derived from NMR analysis. Copyright © 2015 John Wiley & Sons, Ltd. PMID:26248898

  6. Protein folding on the ribosome studied using NMR spectroscopy

    PubMed Central

    Waudby, Christopher A.; Launay, Hélène; Cabrita, Lisa D.; Christodoulou, John

    2013-01-01

    NMR spectroscopy is a powerful tool for the investigation of protein folding and misfolding, providing a characterization of molecular structure, dynamics and exchange processes, across a very wide range of timescales and with near atomic resolution. In recent years NMR methods have also been developed to study protein folding as it might occur within the cell, in a de novo manner, by observing the folding of nascent polypeptides in the process of emerging from the ribosome during synthesis. Despite the 2.3 MDa molecular weight of the bacterial 70S ribosome, many nascent polypeptides, and some ribosomal proteins, have sufficient local flexibility that sharp resonances may be observed in solution-state NMR spectra. In providing information on dynamic regions of the structure, NMR spectroscopy is therefore highly complementary to alternative methods such as X-ray crystallography and cryo-electron microscopy, which have successfully characterized the rigid core of the ribosome particle. However, the low working concentrations and limited sample stability associated with ribosome–nascent chain complexes means that such studies still present significant technical challenges to the NMR spectroscopist. This review will discuss the progress that has been made in this area, surveying all NMR studies that have been published to date, and with a particular focus on strategies for improving experimental sensitivity. PMID:24083462

  7. Design and applications of an in situ electrochemical NMR cell

    NASA Astrophysics Data System (ADS)

    Zhang, Xiaocan; Zwanziger, Josef W.

    2011-01-01

    A device using a three-electrode electrochemical cell (referred to as an ECNMR cell) was successfully constructed that could be used in a standard 5 mm NMR probe to acquire high-resolution NMR spectra while the working electrode was held at a constant electrical potential. The working electrode was a 20 nm thick gold film thermally coated on the outside of an inner 3 mm glass tube. An underlayer consisting of (3-mercaptopropyl)trimethoxy-silane was coated on the glass surface in order to improve its adhesion to gold. Tests showed prolonged life of the gold film. Details of the design and construction of the ECNMR cell are described. The ECNMR cell could be routinely used in a multi-user service high-resolution NMR instrument under oxygen-free conditions in both aqueous and non-aqueous solvents. Different approaches were applied to suppress the noise transmitted between the potentiostat and the NMR spectrometer. These approaches were shown to be effective in reducing background noise in the NMR spectra. The electrochemical and NMR performance of the ECNMR cell is presented. The reduction of 1,4-benzoquinone in both aqueous and non-aqueous solvents was used for testing. The evolution of the in situ ECNMR spectra with time demonstrated that use of the ECNMR cell was feasible. Studies of caffeic acid and 9-chloroanthracene using this ECNMR cell were undertaken to explore its applications, such as monitoring reactions and studying their reaction mechanisms.

  8. Nanoscale NMR spectroscopy and imaging of multiple nuclear species

    NASA Astrophysics Data System (ADS)

    Devience, Stephen J.; Pham, Linh M.; Lovchinsky, Igor; Sushkov, Alexander O.; Bar-Gill, Nir; Belthangady, Chinmay; Casola, Francesco; Corbett, Madeleine; Zhang, Huiliang; Lukin, Mikhail; Park, Hongkun; Yacoby, Amir; Walsworth, Ronald L.

    2015-02-01

    Nuclear magnetic resonance (NMR) spectroscopy and magnetic resonance imaging (MRI) provide non-invasive information about multiple nuclear species in bulk matter, with wide-ranging applications from basic physics and chemistry to biomedical imaging. However, the spatial resolution of conventional NMR and MRI is limited to several micrometres even at large magnetic fields (>1 T), which is inadequate for many frontier scientific applications such as single-molecule NMR spectroscopy and in vivo MRI of individual biological cells. A promising approach for nanoscale NMR and MRI exploits optical measurements of nitrogen-vacancy (NV) colour centres in diamond, which provide a combination of magnetic field sensitivity and nanoscale spatial resolution unmatched by any existing technology, while operating under ambient conditions in a robust, solid-state system. Recently, single, shallow NV centres were used to demonstrate NMR of nanoscale ensembles of proton spins, consisting of a statistical polarization equivalent to ˜100-1,000 spins in uniform samples covering the surface of a bulk diamond chip. Here, we realize nanoscale NMR spectroscopy and MRI of multiple nuclear species (1H, 19F, 31P) in non-uniform (spatially structured) samples under ambient conditions and at moderate magnetic fields (˜20 mT) using two complementary sensor modalities.

  9. ECG gated NMR-CT for cardiovascular diseases

    SciTech Connect

    Nishikawa, J.; Machida, K.; Iio, M.; Yoshimoto, N.; Sugimoto, T.; Kawaguchi, H.; Mano, H.

    1984-01-01

    The authors applied NMR-CT to cardiac study with ECG gated technique to evaluate the left ventricular (LV) function and compared it with cardiovascular nuclear medicine study (NM). The NMR-CT machine has resistive air-core magnet with 0.15 Tesla. The saturation recovery image or inversion recovery image were obtained as 256 x 256 matrix and 15 mm in thickness. The study population was ten patients who were evaluated both by NMR image and by NM performed within one week interval. The heart muscle was able to be visualized without any contrast material nor radioisotopes in inversion recovery images, whereas saturation recovery images failed to separate heart muscle from blood pool. The wall motions of LV in both methods were well correlated except for inferior wall. The values of ejection fraction in NMR image were moderately low, but two modalities showed satisfactory correlation (r=0.85). The region of myocardial infarction was revealed as wall thinning and/or wall motion abnormality. It is still preliminary to draw a conclusion, however, it can be said that in the evaluation of LV function, method by NMR might be of equal value to those of NM. It can be certain that eventually gated NMR-CT will become more effective method for various aspects of cardiovascular evaluation.

  10. NMR-spectroscopic analysis of mixtures: from structure to function

    PubMed Central

    Forseth, Ry R.; Schroeder, Frank C.

    2010-01-01

    NMR spectroscopy as a particularly information-rich method offers unique opportunities for improving the structural and functional characterization of metabolomes, which will be essential for advancing the understanding of many biological processes. Whereas traditionally NMR spectroscopy was mostly relegated to the characterization of pure compounds, the last few years have seen a surge of interest in using NMR spectroscopic techniques for characterizing complex metabolite mixtures. Development of new methods was motivated partly by the realization that using NMR for the analysis of metabolite mixtures can help identify otherwise inaccessible small molecules, for example compounds that are prone to chemical decomposition and thus cannot be isolated. Furthermore, comparative metabolomics and statistical analyses of NMR-spectra have proven highly effective at identifying novel and known metabolites that correlate with changes in genotype or phenotype. In this review, we provide an overview of the range of NMR spectroscopic techniques recently developed for characterizing metabolite mixtures, including methods used in discovery-oriented natural product chemistry, in the study of metabolite biosynthesis and function, or for comparative analyses of entire metabolomes. PMID:21071261

  11. The development of solid-state NMR of membrane proteins

    PubMed Central

    Opella, Stanley J.

    2014-01-01

    Most biological functions are carried out in supramolecular assemblies. As a result of their slow reorientation in solution, these assemblies have been resistant to the widely employed solution NMR approaches. The development of solid-state NMR to first of all overcome the correlation time problem and then obtain informative high-resolution spectra of proteins in supramolecular assemblies, such as virus particles and membranes, is described here. High resolution solid-state NMR is deeply intertwined with the history of NMR, and the seminal paper was published in 1948. Although the general principles were understood by the end of the 1950s, it has taken more than fifty years for instrumentation and experimental methods to become equal to the technical problems presented by the biological assemblies of greatest interest. It is now possible to obtain atomic resolution structures of viral coat proteins in virus particles and membrane proteins in phospholipid bilayers by oriented sample solid-state NMR methods. The development of this aspect of the field of solid-state NMR is summarized in this review article. PMID:26069880

  12. Ultrafast 2D NMR: an emerging tool in analytical spectroscopy.

    PubMed

    Giraudeau, Patrick; Frydman, Lucio

    2014-01-01

    Two-dimensional nuclear magnetic resonance (2D NMR) spectroscopy is widely used in chemical and biochemical analyses. Multidimensional NMR is also witnessing increased use in quantitative and metabolic screening applications. Conventional 2D NMR experiments, however, are affected by inherently long acquisition durations, arising from their need to sample the frequencies involved along their indirect domains in an incremented, scan-by-scan nature. A decade ago, a so-called ultrafast (UF) approach was proposed, capable of delivering arbitrary 2D NMR spectra involving any kind of homo- or heteronuclear correlation, in a single scan. During the intervening years, the performance of this subsecond 2D NMR methodology has been greatly improved, and UF 2D NMR is rapidly becoming a powerful analytical tool experiencing an expanded scope of applications. This review summarizes the principles and main developments that have contributed to the success of this approach and focuses on applications that have been recently demonstrated in various areas of analytical chemistry--from the real-time monitoring of chemical and biochemical processes, to extensions in hyphenated techniques and in quantitative applications. PMID:25014342

  13. NMR analysis on microfluidic devices by remote detection

    SciTech Connect

    McDonnell, Erin E.; Han, SongI; Hilty, Christian; Pierce,Kimberly; Pines, Alexander

    2005-08-15

    We present a novel approach to perform high-sensitivity NMR imaging and spectroscopic analysis on microfluidic devices. The application of NMR, the most information rich spectroscopic technique, to microfluidic devices remains a challenge because the inherently low sensitivity of NMR is aggravated by small fluid volumes leading to low NMR signal, and geometric constraints resulting in poor efficiency for inductive detection. We address the latter by physically separating signal detection from encoding of information with remote detection. Thereby, we use a commercial imaging probe with sufficiently large diameter to encompass the entire device, enabling encoding of NMR information at any location on the chip. Because large-diameter coils are too insensitive for detection, we store the encoded information as longitudinal magnetization and flow it into the outlet capillary. There, we detect the signal with optimal sensitivity using a solenoidal microcoil, and reconstruct the information encoded in the fluid. We present a generally applicable design for a detection-only microcoil probe that can be inserted into the bore of a commercial imaging probe. Using hyperpolarized 129Xe gas, we show that this probe enables sensitive reconstruction of NMR spectroscopic information encoded by the large imaging probe while keeping the flexibility of a large coil.

  14. Ultrafast 2D NMR: An Emerging Tool in Analytical Spectroscopy

    NASA Astrophysics Data System (ADS)

    Giraudeau, Patrick; Frydman, Lucio

    2014-06-01

    Two-dimensional nuclear magnetic resonance (2D NMR) spectroscopy is widely used in chemical and biochemical analyses. Multidimensional NMR is also witnessing increased use in quantitative and metabolic screening applications. Conventional 2D NMR experiments, however, are affected by inherently long acquisition durations, arising from their need to sample the frequencies involved along their indirect domains in an incremented, scan-by-scan nature. A decade ago, a so-called ultrafast (UF) approach was proposed, capable of delivering arbitrary 2D NMR spectra involving any kind of homo- or heteronuclear correlation, in a single scan. During the intervening years, the performance of this subsecond 2D NMR methodology has been greatly improved, and UF 2D NMR is rapidly becoming a powerful analytical tool experiencing an expanded scope of applications. This review summarizes the principles and main developments that have contributed to the success of this approach and focuses on applications that have been recently demonstrated in various areas of analytical chemistry—from the real-time monitoring of chemical and biochemical processes, to extensions in hyphenated techniques and in quantitative applications.

  15. NMR Logging to Estimate Hydraulic Conductivity in Unconsolidated Aquifers.

    PubMed

    Knight, Rosemary; Walsh, David O; Butler, James J; Grunewald, Elliot; Liu, Gaisheng; Parsekian, Andrew D; Reboulet, Edward C; Knobbe, Steve; Barrows, Mercer

    2016-01-01

    Nuclear magnetic resonance (NMR) logging provides a new means of estimating the hydraulic conductivity (K) of unconsolidated aquifers. The estimation of K from the measured NMR parameters can be performed using the Schlumberger-Doll Research (SDR) equation, which is based on the Kozeny-Carman equation and initially developed for obtaining permeability from NMR logging in petroleum reservoirs. The SDR equation includes empirically determined constants. Decades of research for petroleum applications have resulted in standard values for these constants that can provide accurate estimates of permeability in consolidated formations. The question we asked: Can standard values for the constants be defined for hydrogeologic applications that would yield accurate estimates of K in unconsolidated aquifers? Working at 10 locations at three field sites in Kansas and Washington, USA, we acquired NMR and K data using direct-push methods over a 10- to 20-m depth interval in the shallow subsurface. Analysis of pairs of NMR and K data revealed that we could dramatically improve K estimates by replacing the standard petroleum constants with new constants, optimal for estimating K in the unconsolidated materials at the field sites. Most significant was the finding that there was little change in the SDR constants between sites. This suggests that we can define a new set of constants that can be used to obtain high resolution, cost-effective estimates of K from NMR logging in unconsolidated aquifers. This significant result has the potential to change dramatically the approach to determining K for hydrogeologic applications. PMID:25810149

  16. Apparatus for direct addition of reagents into a nuclear magnetic resonance (NMR) sample in the NMR probe

    NASA Astrophysics Data System (ADS)

    Perrin, Charles L.; Rivero, Ignacio A.

    1999-04-01

    Nuclear magnetic resonance (NMR) is a widely used tool in chemistry and biochemistry. It is occasionally necessary to add small aliquots of solvents or reagents repeatedly into the NMR tube. Ordinarily this is accomplished only by ejecting the sample and carrying out the addition outside the probe. It would be preferable to add the aliquot directly into the sample. We have designed and implemented a delivery system to accomplish this. This apparatus is particularly applicable to a recent NMR titration method for measuring relative pK's and to experiments where temperature must also be varied. This apparatus provides a safe, simple, and inexpensive method for repeated aliquot addition directly into the sample in the NMR probe.

  17. LEGO-NMR spectroscopy: a method to visualize individual subunits in large heteromeric complexes.

    PubMed

    Mund, Markus; Overbeck, Jan H; Ullmann, Janina; Sprangers, Remco

    2013-10-18

    Seeing the big picture: Asymmetric macromolecular complexes that are NMR active in only a subset of their subunits can be prepared, thus decreasing NMR spectral complexity. For the hetero heptameric LSm1-7 and LSm2-8 rings NMR spectra of the individual subunits of the complete complex are obtained, showing a conserved RNA binding site. This LEGO-NMR technique makes large asymmetric complexes accessible to detailed NMR spectroscopic studies. PMID:23946163

  18. (13)C NMR assignments of regenerated cellulose from solid-state 2D NMR spectroscopy.

    PubMed

    Idström, Alexander; Schantz, Staffan; Sundberg, Johan; Chmelka, Bradley F; Gatenholm, Paul; Nordstierna, Lars

    2016-10-20

    From the assignment of the solid-state (13)C NMR signals in the C4 region, distinct types of crystalline cellulose, cellulose at crystalline surfaces, and disordered cellulose can be identified and quantified. For regenerated cellulose, complete (13)C assignments of the other carbon regions have not previously been attainable, due to signal overlap. In this study, two-dimensional (2D) NMR correlation methods were used to resolve and assign (13)C signals for all carbon atoms in regenerated cellulose. (13)C-enriched bacterial nanocellulose was biosynthesized, dissolved, and coagulated as highly crystalline cellulose II. Specifically, four distinct (13)C signals were observed corresponding to conformationally different anhydroglucose units: two signals assigned to crystalline moieties and two signals assigned to non-crystalline species. The C1, C4 and C6 regions for cellulose II were fully examined by global spectral deconvolution, which yielded qualitative trends of the relative populations of the different cellulose moieties, as a function of wetting and drying treatments. PMID:27474592

  19. Monitoring prion protein stability by NMR.

    PubMed

    Julien, Olivier; Graether, Steffen P; Sykes, Brian D

    2009-01-01

    Prion diseases, or transmissible spongiform encephalopathies (TSE), are a group of fatal neurological diseases that affect both humans and animals. At the end of the 20th century, bovine spongiform encephalopathy (BSE), better known as mad cow disease, was shown to be transmissible to humans. This resulted in considerable concern for public health and a number of questions for scientists. The first question answered was the possible source of the disease, which appears to be the prion protein (PrP). There are two major forms of this protein: the native, noninfectious form (PrP(C)), and the misfolded infectious form (PrP(Sc)). PrP(C) is mainly alpha-helical in structure, whereas PrP(Sc) aggregates into an assembly of beta-sheets, forming amyloid fibrils. Since the first solution structure of the noninfectious form of the mouse prion protein, about 30 structures of the globular portion of PrP(C) have been characterized from different organisms. However, only a few minor differences are observed when comparing one PrP(C) structure to another. The key to understanding prion formation may then be not in the structure of PrP(C), but in the mechanism underlying PrP(C) unfolding and then conversion into a misfolded fibril state. To identify the possible region(s) of PrP(C) responsible for initiating the conversion into the amyloid fibril formation, nuclear magnetic resonance (NMR) was applied to characterize the stability and structure of PrP(C) and intermediate states during the conversion from PrP(C) to PrP(Sc). Subsequently urea was used to induce unfolding, and data analysis revealed region-specific structural stabilities that may bring insights into the mechanisms underlying conversion of protein into an infectious prion. PMID:19697241

  20. Accessible surface area from NMR chemical shifts.

    PubMed

    Hafsa, Noor E; Arndt, David; Wishart, David S

    2015-07-01

    Accessible surface area (ASA) is the surface area of an atom, amino acid or biomolecule that is exposed to solvent. The calculation of a molecule's ASA requires three-dimensional coordinate data and the use of a "rolling ball" algorithm to both define and calculate the ASA. For polymers such as proteins, the ASA for individual amino acids is closely related to the hydrophobicity of the amino acid as well as its local secondary and tertiary structure. For proteins, ASA is a structural descriptor that can often be as informative as secondary structure. Consequently there has been considerable effort over the past two decades to try to predict ASA from protein sequence data and to use ASA information (derived from chemical modification studies) as a structure constraint. Recently it has become evident that protein chemical shifts are also sensitive to ASA. Given the potential utility of ASA estimates as structural constraints for NMR we decided to explore this relationship further. Using machine learning techniques (specifically a boosted tree regression model) we developed an algorithm called "ShiftASA" that combines chemical-shift and sequence derived features to accurately estimate per-residue fractional ASA values of water-soluble proteins. This method showed a correlation coefficient between predicted and experimental values of 0.79 when evaluated on a set of 65 independent test proteins, which was an 8.2 % improvement over the next best performing (sequence-only) method. On a separate test set of 92 proteins, ShiftASA reported a mean correlation coefficient of 0.82, which was 12.3 % better than the next best performing method. ShiftASA is available as a web server ( http://shiftasa.wishartlab.com ) for submitting input queries for fractional ASA calculation. PMID:26078090

  1. A comparison of calculated NMR shielding probes.

    PubMed

    Martin, Ned H; Loveless, David M; Wade, Dustin C

    2004-12-01

    In a strong magnetic field, covalently bonded hydrogen nuclei located over the plane of an anisotropic pi bond-containing functional group experience magnetic shielding (or deshielding) that results from the combined effect of the magnetic anisotropy of the functional group and other nearby covalent bonds plus other intramolecular shielding effects. These effects can now be calculated with reasonable accuracy using ab initio methods. We have investigated several computational probes of the magnetic shielding surface near anisotropic functional groups and compared the results to previous reports of experimental observations in example structures. GIAO-HF in Gaussian 03 was employed to calculate isotropic shielding values and to predict the net NMR shielding increment for several computational probes: methane, diatomic hydrogen, a hydrogen atom, a helium atom, or a ghost atom, each held in various positions over simple test molecules (ethene, ethyne, benzene and HCN) that contain the functional groups studied. Also, the effect of performing single point calculations versus constrained geometry-optimized calculations was examined. In addition, the effect of the angle of the orientation of the probe molecule (in the case of CH(4) and H(2)) relative to the pi bond in the test molecule was studied. Finally, the atomic charges in the molecular probes (CH(4) and H(2)) were computed to investigate the nature of the interaction of the probe with the test molecule. The optimal, most economical computational results were obtained using single point calculations of a diatomic hydrogen probe oriented perpendicular to the surface (or axis) of the test molecule. PMID:15530824

  2. Whole-core analysis by sup 13 C NMR

    SciTech Connect

    Vinegar, H.J.; Tutunjian, P.N. ); Edelstein, W.A.; Roemer, P.B. )

    1991-06-01

    This paper reports on a whole-core nuclear magnetic resonance (NMR) system that was used to obtain natural abundance {sup 13}C spectra. The system enables rapid, nondestructive measurements of bulk volume of movable oil, aliphatic/aromatic ratio, oil viscosity, and organic vs. carbonate carbon. {sup 13}C NMR can be used in cores where the {sup 1}H NMR spectrum is too broad to resolve oil and water resonances separately. A 5 1/4-in. {sup 13}C/{sup 1}H NMR coil was installed on a General Electric (GE) CSI-2T NMR imager/spectrometer. With a 4-in.-OD whole core, good {sup 13}C signal/noise ratio (SNR) is obtained within minutes, while {sup 1}H spectra are obtained in seconds. NMR measurements have been made of the {sup 13}C and {sup 1}H density of crude oils with a wide range of API gravities. For light- and medium-gravity oils, the {sup 13}C and {sup 1}H signal per unit volume is constant within about 3.5%. For heavy crudes, the {sup 13}C and {sup 1}H density measured by NMR is reduced by the shortening of spin-spin relaxation time. {sup 13}C and {sup 1}H NMR spin-lattice relaxation times were measured on a suite of Cannon viscosity standards, crude oils (4 to 60{degrees} API), and alkanes (C{sub 5} through C{sub 16}) with viscosities at 77{degrees}F ranging from 0.5 cp to 2.5 {times} 10{sup 7} cp. The {sup 13}C and {sup 1}H relaxation times show a similar correlation with viscosity from which oil viscosity can be estimated accurately for viscosities up to 100 cp. The {sup 13}C surface relaxation rate for oils on water-wet rocks is very low. Nonproton decoupled {sup 13}C NMR is shown to be insensitive to kerogen; thus, {sup 13}C NMR measures only the movable hydrocarbon content of the cores. In carbonates, the {sup 13}C spectrum also contains a carbonate powder pattern useful in quantifying inorganic carbon and distinguishing organic from carbonate carbon.

  3. Ultra-wideline solid-state NMR spectroscopy.

    PubMed

    Schurko, Robert W

    2013-09-17

    Although solid-state NMR (SSNMR) provides rich information about molecular structure and dynamics, the small spin population differences between pairs of spin states that give rise to NMR transitions make it an inherently insensitive spectroscopic technique in terms of signal acquisition. Scientists have continuously addressed this issue via improvements in NMR hardware and probes, increases in the strength of the magnetic field, and the development of innovative pulse sequences and acquisition methodologies. As a result, researchers can now study NMR-active nuclides previously thought to be unobservable or too unreceptive for routine examination via SSNMR. Several factors can make it extremely challenging to detect signal or acquire spectra using SSNMR: (i) low gyromagnetic ratios (i.e., low Larmor frequencies), (ii) low natural abundances or dilution of the nuclide of interest (e.g., metal nuclides in proteins or in organometallic catalysts supported on silica), (iii) inconvenient relaxation characteristics (e.g., very long longitudinal or very short transverse relaxation times), and/or (iv) extremely broad powder patterns arising from large anisotropic NMR interactions. Our research group has been particularly interested in efficient acquisition of broad NMR powder patterns for a variety of spin-1/2 and quadrupolar (spin > 1/2) nuclides. Traditionally, researchers have used the term "wideline" NMR to refer to experiments yielding broad (1)H and (2)H SSNMR spectra ranging from tens of kHz to ∼250 kHz in breadth. With modern FT NMR hardware, uniform excitation in these spectral ranges is relatively easy, allowing for the acquisition of high quality spectra. However, spectra that range in breadth from ca. 250 kHz to tens of MHz cannot be uniformly excited with conventional, high-power rectangular pulses. Rather, researchers must apply special methodologies to acquire such spectra, which have inherently low S/N because the signal intensity is spread across such

  4. GEL-STATE NMR OF BALL-MILLED WHOLE CELL WALLS IN DMSO-d6 USING 2D SOLUTION-STATE NMR SPECTROSCOPY

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plant cell walls were used for obtaining 2D solution-state NMR spectra without actual solubilization or structural modification. Ball-milled whole cell walls were swelled directly in the NMR tube with DMSO-d6 where they formed a gel. There are relatively few gel-state NMR studies. Most have involved...

  5. Transient protein-protein interactions visualized by solution NMR.

    PubMed

    Liu, Zhu; Gong, Zhou; Dong, Xu; Tang, Chun

    2016-01-01

    Proteins interact with each other to establish their identities in cell. The affinities for the interactions span more than ten orders of magnitude, and KD values in μM-mM regimen are considered transient and are important in cell signaling. Solution NMR including diamagnetic and paramagnetic techniques has enabled atomic-resolution depictions of transient protein-protein interactions. Diamagnetic NMR allows characterization of protein complexes with KD values up to several mM, whereas ultraweak and fleeting complexes can be modeled with the use of paramagnetic NMR especially paramagnetic relaxation enhancement (PRE). When tackling ever-larger protein complexes, PRE can be particularly useful in providing long-range intermolecular distance restraints. As NMR measurements are averaged over the ensemble of complex structures, structural information for dynamic protein-protein interactions besides the stereospecific one can often be extracted. Herein the protein interaction dynamics are exemplified by encounter complexes, alternative binding modes, and coupled binding/folding of intrinsically disordered proteins. Further integration of NMR with other biophysical techniques should allow better visualization of transient protein-protein interactions. In particular, single-molecule data may facilitate the interpretation of ensemble-averaged NMR data. Though same structures of proteins and protein complexes were found in cell as in diluted solution, we anticipate that the dynamics of transient protein protein-protein interactions be different, which awaits awaits exploration by NMR. This article is part of a Special Issue entitled: Physiological Enzymology and Protein Functions. This article is part of a Special Issue entitled: Physiological Enzymology and Protein Functions. PMID:25896389

  6. Accurate, fully-automated NMR spectral profiling for metabolomics.

    PubMed

    Ravanbakhsh, Siamak; Liu, Philip; Bjorndahl, Trent C; Bjordahl, Trent C; Mandal, Rupasri; Grant, Jason R; Wilson, Michael; Eisner, Roman; Sinelnikov, Igor; Hu, Xiaoyu; Luchinat, Claudio; Greiner, Russell; Wishart, David S

    2015-01-01

    Many diseases cause significant changes to the concentrations of small molecules (a.k.a. metabolites) that appear in a person's biofluids, which means such diseases can often be readily detected from a person's "metabolic profile"-i.e., the list of concentrations of those metabolites. This information can be extracted from a biofluids Nuclear Magnetic Resonance (NMR) spectrum. However, due to its complexity, NMR spectral profiling has remained manual, resulting in slow, expensive and error-prone procedures that have hindered clinical and industrial adoption of metabolomics via NMR. This paper presents a system, BAYESIL, which can quickly, accurately, and autonomously produce a person's metabolic profile. Given a 1D 1H NMR spectrum of a complex biofluid (specifically serum or cerebrospinal fluid), BAYESIL can automatically determine the metabolic profile. This requires first performing several spectral processing steps, then matching the resulting spectrum against a reference compound library, which contains the "signatures" of each relevant metabolite. BAYESIL views spectral matching as an inference problem within a probabilistic graphical model that rapidly approximates the most probable metabolic profile. Our extensive studies on a diverse set of complex mixtures including real biological samples (serum and CSF), defined mixtures and realistic computer generated spectra; involving > 50 compounds, show that BAYESIL can autonomously find the concentration of NMR-detectable metabolites accurately (~ 90% correct identification and ~ 10% quantification error), in less than 5 minutes on a single CPU. These results demonstrate that BAYESIL is the first fully-automatic publicly-accessible system that provides quantitative NMR spectral profiling effectively-with an accuracy on these biofluids that meets or exceeds the performance of trained experts. We anticipate this tool will usher in high-throughput metabolomics and enable a wealth of new applications of NMR in

  7. Solid-state NMR characterization of Mowry Formation shales

    SciTech Connect

    Miknis, F.P.

    1992-04-01

    Solid-state {sup 13}C and {sup 29}Si NMR measurements were carried out on a series of petroleum source rocks from the Mowry Formation of the Powder River Basin in Wyoming. The objectives of this study wereto use CP/MAS {sup 13}C NMR measurements to monitor changes in the carbon structure of the kerogen that result from depth of burial, and to examine the feasibility of {sup 29}Si NMR for studying the thermal alteration of clay minerals during diagenesis. Carbon and silicon NMR measurements were made on a suite of samples covering a present-day depth interval of 3,000 to 11,500 ft.In general, the NMR results endorsed other geochemical analyses that were performed on the source rocks as part of another study to examine pressure compartmentalization in the Mowry Formation. The carbon aromaticity of the kerogen increased with depth of burial, and at depths greater that approximately 10,000 ft the kerogen showed little capacity to generate additional oil because of the small fraction of residual aliphatic carbon. By combining NMR and Rock-Eval measurements, an estimate of the hydrogen budget was obtained. The calculations indicated that approximately 20% of the kerogen was converted to hydrocarbons, and that sufficient hydrogen was liberated from aromatization and condensation reactions to stabilize the generated products. The {sup 29}Si NMR spectra were characterized by a relatively sharp quartz resonance and a broad resonance from the clay minerals. With increasing depth of burial, the clay resonance became broader and shifted slightly downfield. These changes qualitatively support X-ray analysis that shows progressive alteration of illite to smectite with depth of burial.

  8. Solid-state NMR characterization of Mowry Formation shales

    SciTech Connect

    Miknis, F.P.

    1992-04-01

    Solid-state [sup 13]C and [sup 29]Si NMR measurements were carried out on a series of petroleum source rocks from the Mowry Formation of the Powder River Basin in Wyoming. The objectives of this study wereto use CP/MAS [sup 13]C NMR measurements to monitor changes in the carbon structure of the kerogen that result from depth of burial, and to examine the feasibility of [sup 29]Si NMR for studying the thermal alteration of clay minerals during diagenesis. Carbon and silicon NMR measurements were made on a suite of samples covering a present-day depth interval of 3,000 to 11,500 ft.In general, the NMR results endorsed other geochemical analyses that were performed on the source rocks as part of another study to examine pressure compartmentalization in the Mowry Formation. The carbon aromaticity of the kerogen increased with depth of burial, and at depths greater that approximately 10,000 ft the kerogen showed little capacity to generate additional oil because of the small fraction of residual aliphatic carbon. By combining NMR and Rock-Eval measurements, an estimate of the hydrogen budget was obtained. The calculations indicated that approximately 20% of the kerogen was converted to hydrocarbons, and that sufficient hydrogen was liberated from aromatization and condensation reactions to stabilize the generated products. The [sup 29]Si NMR spectra were characterized by a relatively sharp quartz resonance and a broad resonance from the clay minerals. With increasing depth of burial, the clay resonance became broader and shifted slightly downfield. These changes qualitatively support X-ray analysis that shows progressive alteration of illite to smectite with depth of burial.

  9. NMR Study of Strontium Binding by a Micaceous Mineral

    SciTech Connect

    Bowers, Geoffrey M.; Ravella, Ramesh; Komarneni, S.; Mueller, Karl T.

    2006-04-13

    The nature of strontium binding by soil minerals directly affects the transport and sequestration/remediation of radioactive strontium species released from leaking high-level nuclear waste storage tanks. However, the molecular-level structure of strontium binding sites has seldom been explored in phyllosilicate minerals by direct spectroscopic means and is not well-understood. In this work, we use solid-state NMR to analyze strontium directly and indirectly in a fully strontium-exchanged synthetic mica of nominal composition Na4Mg6Al4Si4O20F4. Thermogravimetric analysis, X-ray diffraction analysis, and NMR evidence supports that heat treatment at 500 °C for 4 h fully dehydrates the mica, creating a hydrogen-free interlayer. Analysis of the strontium NMR spectrum of the heat-treated mica shows a single strontium environment with a quadrupolar coupling constant of 9.02 MHz and a quadrupolar asymmetry parameter of 1.0. These quadrupolar parameters are consistent with a highly distorted and asymmetric coordination environment that would be produced by strontium cations without water in the coordination sphere bound deep within the ditrigonal holes. Evidence for at least one additional strontium environment, where proton-strontium couplings may occur, was found via a 1H-87Sr transfer of populations by double resonance NMR experiment. We conclude that the strontium cations in the proton-free interlayer are observable by 87Sr NMR and bound through electrostatic interactions as nine coordinate inner-sphere complexes sitting in the ditrigonal holes. Partially hydrated strontium cations invisible to direct 87Sr NMR are also present and located on the external mica surfaces, which are known to hydrate upon exposure to atmospheric moisture. These results demonstrate that modern pulsed NMR techniques and high fields can be used effectively to provide structural details of strontium binding by phyllosilicate minerals.

  10. Molecular dynamics simulations on PGLa using NMR orientational constraints.

    PubMed

    Sternberg, Ulrich; Witter, Raiker

    2015-11-01

    NMR data obtained by solid state NMR from anisotropic samples are used as orientational constraints in molecular dynamics simulations for determining the structure and dynamics of the PGLa peptide within a membrane environment. For the simulation the recently developed molecular dynamics with orientational constraints technique (MDOC) is used. This method introduces orientation dependent pseudo-forces into the COSMOS-NMR force field. Acting during a molecular dynamics simulation these forces drive molecular rotations, re-orientations and folding in such a way that the motional time-averages of the tensorial NMR properties are consistent with the experimentally measured NMR parameters. This MDOC strategy does not depend on the initial choice of atomic coordinates, and is in principle suitable for any flexible and mobile kind of molecule; and it is of course possible to account for flexible parts of peptides or their side-chains. MDOC has been applied to the antimicrobial peptide PGLa and a related dimer model. With these simulations it was possible to reproduce most NMR parameters within the experimental error bounds. The alignment, conformation and order parameters of the membrane-bound molecule and its dimer were directly derived with MDOC from the NMR data. Furthermore, this new approach yielded for the first time the distribution of segmental orientations with respect to the membrane and the order parameter tensors of the dimer systems. It was demonstrated the deuterium splittings measured at the peptide to lipid ratio of 1/50 are consistent with a membrane spanning orientation of the peptide. PMID:26358333

  11. Quantitative analysis of protein-ligand interactions by NMR.

    PubMed

    Furukawa, Ayako; Konuma, Tsuyoshi; Yanaka, Saeko; Sugase, Kenji

    2016-08-01

    Protein-ligand interactions have been commonly studied through static structures of the protein-ligand complex. Recently, however, there has been increasing interest in investigating the dynamics of protein-ligand interactions both for fundamental understanding of the underlying mechanisms and for drug development. NMR is a versatile and powerful tool, especially because it provides site-specific quantitative information. NMR has widely been used to determine the dissociation constant (KD), in particular, for relatively weak interactions. The simplest NMR method is a chemical-shift titration experiment, in which the chemical-shift changes of a protein in response to ligand titration are measured. There are other quantitative NMR methods, but they mostly apply only to interactions in the fast-exchange regime. These methods derive the dissociation constant from population-averaged NMR quantities of the free and bound states of a protein or ligand. In contrast, the recent advent of new relaxation-based experiments, including R2 relaxation dispersion and ZZ-exchange, has enabled us to obtain kinetic information on protein-ligand interactions in the intermediate- and slow-exchange regimes. Based on R2 dispersion or ZZ-exchange, methods that can determine the association rate, kon, dissociation rate, koff, and KD have been developed. In these approaches, R2 dispersion or ZZ-exchange curves are measured for multiple samples with different protein and/or ligand concentration ratios, and the relaxation data are fitted to theoretical kinetic models. It is critical to choose an appropriate kinetic model, such as the two- or three-state exchange model, to derive the correct kinetic information. The R2 dispersion and ZZ-exchange methods are suitable for the analysis of protein-ligand interactions with a micromolar or sub-micromolar dissociation constant but not for very weak interactions, which are typical in very fast exchange. This contrasts with the NMR methods that are used

  12. NMR imaging and cryoporometry of swelling clays

    NASA Astrophysics Data System (ADS)

    Dvinskikh, Sergey V.; Szutkowski, Kosma; Petrov, Oleg V.; Furó, István.

    2010-05-01

    strength as well as investigating the effect of the confining geometry and material surface properties seem to be worth to pursue. Acknowledgements: This work has been supported by the Swedish Nuclear Fuel and Waste Management Co (SKB) and the Swedish Research Council VR. References: [1] Dvinskikh S. V., Szutkowski K., Furó I. MRI profiles over a very wide concentration ranges: application to swelling of a bentonite clay. J. Magn. Reson. 198, 146 (2009). [2] Petrov O. V., Furó I. NMR cryoporometry: Principles, applications and potential. Prog. Nucl. Magn. Reson. Spec. 54, 97 (2009).

  13. Mechanisms of amyloid formation revealed by solution NMR

    PubMed Central

    Karamanos, Theodoros K.; Kalverda, Arnout P.; Thompson, Gary S.; Radford, Sheena E.

    2015-01-01

    Amyloid fibrils are proteinaceous elongated aggregates involved in more than fifty human diseases. Recent advances in electron microscopy and solid state NMR have allowed the characterization of fibril structures to different extents of refinement. However, structural details about the mechanism of fibril formation remain relatively poorly defined. This is mainly due to the complex, heterogeneous and transient nature of the species responsible for assembly; properties that make them difficult to detect and characterize in structural detail using biophysical techniques. The ability of solution NMR spectroscopy to investigate exchange between multiple protein states, to characterize transient and low-population species, and to study high molecular weight assemblies, render NMR an invaluable technique for studies of amyloid assembly. In this article we review state-of-the-art solution NMR methods for investigations of: (a) protein dynamics that lead to the formation of aggregation-prone species; (b) amyloidogenic intrinsically disordered proteins; and (c) protein–protein interactions on pathway to fibril formation. Together, these topics highlight the power and potential of NMR to provide atomic level information about the molecular mechanisms of one of the most fascinating problems in structural biology. PMID:26282197

  14. Development of a superconducting bulk magnet for NMR and MRI

    NASA Astrophysics Data System (ADS)

    Nakamura, Takashi; Tamada, Daiki; Yanagi, Yousuke; Itoh, Yoshitaka; Nemoto, Takahiro; Utumi, Hiroaki; Kose, Katsumi

    2015-10-01

    A superconducting bulk magnet composed of six vertically stacked annular single-domain c-axis-oriented Eu-Ba-Cu-O crystals was energized to 4.74 T using a conventional superconducting magnet for high-resolution NMR spectroscopy. Shim coils, gradient coils, and radio frequency coils for high resolution NMR and MRI were installed in the 23 mm-diameter room-temperature bore of the bulk magnet. A 6.9 ppm peak-to-peak homogeneous region suitable for MRI was achieved in the central cylindrical region (6.2 mm diameter, 9.1 mm length) of the bulk magnet by using a single layer shim coil. A 21 Hz spectral resolution that can be used for high resolution NMR spectroscopy was obtained in the central cylindrical region (1.3 mm diameter, 4 mm length) of the bulk magnet by using a multichannel shim coil. A clear 3D MR image dataset of a chemically fixed mouse fetus with (50 μm)3 voxel resolution was obtained in 5.5 h. We therefore concluded that the cryogen-free superconducting bulk magnet developed in this study is useful for high-resolution desktop NMR, MRI and mobile NMR device.

  15. Development of a superconducting bulk magnet for NMR and MRI.

    PubMed

    Nakamura, Takashi; Tamada, Daiki; Yanagi, Yousuke; Itoh, Yoshitaka; Nemoto, Takahiro; Utumi, Hiroaki; Kose, Katsumi

    2015-10-01

    A superconducting bulk magnet composed of six vertically stacked annular single-domain c-axis-oriented Eu-Ba-Cu-O crystals was energized to 4.74 T using a conventional superconducting magnet for high-resolution NMR spectroscopy. Shim coils, gradient coils, and radio frequency coils for high resolution NMR and MRI were installed in the 23 mm-diameter room-temperature bore of the bulk magnet. A 6.9 ppm peak-to-peak homogeneous region suitable for MRI was achieved in the central cylindrical region (6.2 mm diameter, 9.1 mm length) of the bulk magnet by using a single layer shim coil. A 21 Hz spectral resolution that can be used for high resolution NMR spectroscopy was obtained in the central cylindrical region (1.3 mm diameter, 4 mm length) of the bulk magnet by using a multichannel shim coil. A clear 3D MR image dataset of a chemically fixed mouse fetus with (50 μm)(3) voxel resolution was obtained in 5.5 h. We therefore concluded that the cryogen-free superconducting bulk magnet developed in this study is useful for high-resolution desktop NMR, MRI and mobile NMR device. PMID:26295170

  16. Diamond deposition and defect chemistry studied via solid state NMR

    NASA Astrophysics Data System (ADS)

    Gleason, Karen K.

    1994-06-01

    Diamond defects were quantified by nuclear magnetic resonance (NMR). While maintaining the macroscopic integrity of the films, concentrations between 0.001 and 1.0 at.% H were measured, among the lowest ever reported by solid-state 1H NMR. These concentrations were correlated to infrared absorption in the 8 to 10 micron region and to thermal conductivity. Despite the low concentrations, Multiple Quantum NMR reveals a high degree of hydrogen clustering consistent with grain boundary passivation. Most hydrogen is rigidly held, but some, probably in -OCH3 and -NCH3 defects, undergoes rotation at room temperature. Similar results were obtained for hot-filament, microwave-plasma and DC arc-jet films, suggesting a common surface chemistry, but no hydrogen was detected in an as-deposited combustion film. 13C NMR provided the first quantitative determination of non-diamond bonded carbon defects, providing a benchmark for Raman spectroscopy, the primary characterization method for diamond. Selective 13C labeling demonstrated heterogeneous reactions involving carbon occur at the hot-filament. With high-speed magic-angle-spinning 19F NMR, CFx (x=1-3) functionalities were resolved on the surface of plasma-treated diamond powder. Understanding these defects impacts the understanding of film growth mechanisms and structure-property relationships for CVD diamond.

  17. NMR study of the potential composition of Titan's lakes

    NASA Astrophysics Data System (ADS)

    He, Chao; Smith, Mark A.

    2015-05-01

    A large number of hydrocarbon lakes have been discovered in Titan's surface. However, the chemical composition and physical properties of these lakes are not fully understood. We investigate the potential composition of Titan's lakes by NMR. Based upon NMR data, the 1H and 13C NMR spectra of the hydrocarbons in Titan's lakes are simulated on a 1 T spectrometer [being developed at the NASA Jet Propulsion Laboratory (JPL) for future in situ characterization of Titan's lakes]. The study indicates that the dominant composition (all components>1% of the lake composition by mole fraction) in Titan's lakes can be determined and the major soluble organics quantitatively identified from either quantitative 1H or 13C spectra on a 1 T NMR spectrometer. The proton T1 relaxation times are determined for a number of candidate organics in hydrocarbon solution, a necessary determinant for quantitative NMR. The gas solubility of these organics is also investigated to understand the equilibrium of composition between Titan's lakes and atmosphere and the precipitation rates of the molecules at Titan's ground level. Our results are significant for the ongoing discussion regarding the development of in situ, low bias analysis methods and instruments for Titan missions and other outer planet exploration.

  18. Determination of fat content in NMR images of meat

    NASA Astrophysics Data System (ADS)

    Ballerini, Lucia

    2000-12-01

    In this paper we present an application to food science of image processing technique. We describe a method for determining fat content in beef meat. The industry of meat faces a permanent need for improved methods for meat quality evaluation. Researchers want improved techniques to deepen their understanding of meat features. Expectations of consumers for meat quality grow constantly, which induces the necessity of quality control. Recent advances in the area of computer and video processing have created new ways to monitor quality in the food industry. We investigate the use of a new technology to control the quality of food: NMR imaging. The inherent advantages of NMR images are many. Chief among these unprecedented contrasts between the various structures present in meat like muscle, fat, and connective tissue. Moreover, the three-dimensional nature of the NMR method allow us to analyze isolated cross-sectional slices of the meat and to measure the volumetric content of fat, not only the fat visible on the surface. We propose a segmentation algorithm for the detection of fat together with a filtering technique to remove intensity inhomogeneities in NMR images caused by non-uniformities of the magnetic field during acquisition. Measurements have been successfully correlated with chemical analysis and digital photography. Results show that the NMR technique is a promising non-invasive method to determine the fat content in meat.

  19. 15N chemical shift referencing in solid state NMR.

    PubMed

    Bertani, Philippe; Raya, Jésus; Bechinger, Burkhard

    2014-01-01

    Solid-state NMR spectroscopy has much advanced during the last decade and provides a multitude of data that can be used for high-resolution structure determination of biomolecules, polymers, inorganic compounds or macromolecules. In some cases the chemical shift referencing has become a limiting factor to the precision of the structure calculations and we have therefore evaluated a number of methods used in proton-decoupled (15)N solid-state NMR spectroscopy. For (13)C solid-state NMR spectroscopy adamantane is generally accepted as an external standard, but to calibrate the (15)N chemical shift scale several standards are in use. As a consequence the published chemical shift values exhibit considerable differences (up to 22 ppm). In this paper we report the (15)N chemical shift of several commonly used references compounds in order to allow for comparison and recalibration of published data and future work. We show that (15)NH4Cl in its powdered form (at 39.3 ppm with respect to liquid NH3) is a suitable external reference as it produces narrow lines when compared to other reference compounds and at the same time allows for the set-up of cross-polarization NMR experiments. The compound is suitable to calibrate magic angle spinning and static NMR experiments. Finally the temperature variation of (15)NH4Cl chemical shift is reported. PMID:24746715

  20. First Principles NMR Study of Fluorapatite under Pressure

    PubMed Central

    Pavan, Barbara; Ceresoli, Davide; Tecklenburg, Mary M. J.; Fornari, Marco

    2012-01-01

    NMR is the technique of election to probe the local properties of materials. Herein we present the results of density functional theory (DFT) ab initio calculations of the NMR parameters for fluorapatite (FAp), a calcium orthophosphate mineral belonging to the apatite family, by using the GIPAW method [Pickard and Mauri, 2001]. Understanding the local effects of pressure on apatites is particularly relevant because of their important role in many solid state and biomedical applications. Apatites are open structures, which can undergo complex anisotropic deformations, and the response of NMR can elucidate the microscopic changes induced by an applied pressure. The computed NMR parameters proved to be in good agreement with the available experimental data. The structural evaluation of the material behavior under hydrostatic pressure (from −5 to +100 kbar) indicated a shrinkage of the diameter of the apatitic channel, and a strong correlation between NMR shielding and pressure, proving the sensitivity of this technique to even small changes in the chemical environment around the nuclei. This theoretical approach allows the exploration of all the different nuclei composing the material, thus providing a very useful guidance in the interpretation of experimental results, particularly valuable for the more challenging nuclei such as 43Ca and 17O. PMID:22770669

  1. Selective NMR excitation in strongly inhomogeneous magnetic fields.

    PubMed

    Todica, M; Fechete, R; Blümich, B

    2003-10-01

    The NMR-MOUSE is a unilateral and mobile NMR sensor which operates with highly inhomogeneous magnetic fields. To produce a mobile NMR unit, RF excitation is sought, which can be produced with the most simple equipment, in particular nonlinear, low-power amplifiers, and to observe a free induction decay in strongly inhomogeneous fields, the excitation needs to be selective. The possibility to produce selective excitation by sequences of hard low-power radiofrequency pulses in the strongly inhomogeneous magnetic fields of the NMR-MOUSE is explored. The use of the DANTE sequence for selection of magnetization from parts of the sensitive volume was investigated for longitudinal and transverse magnetization by computer simulations and experiments. The spectra of the recorded FIDs and echo signals are in good agreement with those simulated for the excitation, which verifies the concept of the DANTE excitation. The results obtained are an important step towards a low-power operation of the NMR-MOUSE to improve its mobility. PMID:14511590

  2. Low Cost CE-NMR with Microcoils for Chemical Detection

    SciTech Connect

    Adams, K; Klunder, G; Demas, V; Malba, V; Bernhardt, A; Evan, L; Harvey, C; Maxwell, R; Herberg, J L

    2009-01-08

    Understanding speciation in solids and solutions is important for environmental and toxicological purposes. Capillary electrophoresis (CE) is a simple rapid separation technique that can be used to identify species in solution. CE is particularly is well suited for rapid separations of metal containing samples. Direct on-capillary measurement of metal compound speciation can be obtained with nuclear magnetic resonance (NMR). The development of a low-cost microcoil CE-NMR system for in situ characterization of samples of interest is discussed. High precision laser lithography is used to produce copper sputtered microcoils that have comparable resistivity and quality factors to that of hand wound microcoils. A portable NMR system coupled with a CE system has the potential to identify chemical species in aqueous solutions. In addition, transient isotachophoresis can separate and pre-concentrate samples of interest to obtain separate chemical peaks for speciation by online NMR analysis. We are developing separation assays to determine the speciation of chemical complexes in solutions with minimal perturbation to the original sample equilibrium. On-line NMR measurements will be made downstream of the UV detector.

  3. Low Cost CE-NMR with Microcoils for Chemical Detection

    SciTech Connect

    Adams, K L; Klunder, G; Demas, V; Malba, V; Bernhardt, A; Evan, L; Harvey, C; Maxwell, R; Herberg, J

    2008-07-25

    Understanding speciation in solids and solutions is important for environmental and toxicological purposes. Capillary electrophoresis (CE) is a simple rapid separation technique that can be used to identify species in solution. CE is particularly is well suited for rapid separations of metal containing samples. Direct on-capillary measurement of metal compound speciation can be obtained with nuclear magnetic resonance (NMR). The development of a low-cost microcoil CE-NMR system for in situ characterization of samples of interest is discussed. High precision laser lithography is used to produce copper sputtered microcoils that have comparable resistivity and quality factors to that of hand wound microcoils. A portable NMR system coupled with a CE system has the potential to identify chemical species in aqueous solutions. In addition, transient isotachophoresis can separate and pre-concentrate samples of interest to obtain separate chemical peaks for speciation by online NMR analysis. We are developing separation assays to determine the speciation of chemical complexes in solutions with minimal perturbation to the original sample equilibrium. On-line NMR measurements will be made downstream of the UV detector.

  4. GFT projection NMR spectroscopy for proteins in the solid state

    PubMed Central

    Franks, W. Trent; Atreya, Hanudatta S.; Szyperski, Thomas

    2011-01-01

    Recording of four-dimensional (4D) spectra for proteins in the solid state has opened new avenues to obtain virtually complete resonance assignments and three-dimensional (3D) structures of proteins. As in solution state NMR, the sampling of three indirect dimensions leads per se to long minimal measurement time. Furthermore, artifact suppression in solid state NMR relies primarily on radio-frequency pulse phase cycling. For an n-step phase cycle, the minimal measurement times of both 3D and 4D spectra are increased n times. To tackle the associated ‘sampling problem’ and to avoid sampling limited data acquisition, solid state G-Matrix Fourier Transform (SS GFT) projection NMR is introduced to rapidly acquire 3D and 4D spectral information. Specifically, (4,3)D (HA)CANCOCX and (3,2)D (HACA)NCOCX were implemented and recorded for the 6 kDa protein GB1 within about 10% of the time required for acquiring the conventional congeners with the same maximal evolution times and spectral widths in the indirect dimensions. Spectral analysis was complemented by comparative analysis of expected spectral congestion in conventional and GFT NMR experiments, demonstrating that high spectral resolution of the GFT NMR experiments enables one to efficiently obtain nearly complete resonance assignments even for large proteins. PMID:21052779

  5. Intermediate couplings: NMR at the solids-liquids interface

    NASA Astrophysics Data System (ADS)

    Spence, Megan

    2006-03-01

    Anisotropic interactions like dipolar couplings and chemical shift anisotropy have long offered solid-state NMR spectroscopists valuable structural information. Recently, solution-state NMR structural studies have begun to exploit residual dipolar couplings of biological molecules in weakly anisotropic solutions. These residual couplings are about 0.1% of the coupling magnitudes observed in the solid state, allowing simple, high-resolution NMR spectra to be retained. In this work, we examine the membrane-associated opioid, leucine enkephalin (lenk), in which the ordering is ten times larger than that for residual dipolar coupling experiments, requiring a combination of solution-state and solid-state NMR techniques. We adapted conventional solid-state NMR techniques like adiabatic cross- polarization and REDOR for use with such a system, and measured small amide bond dipolar couplings in order to determine the orientation of the amide bonds (and therefore the peptide) with respect to the membrane surface. However, the couplings measured indicate large structural rearrangements on the surface and contradict the published structures obtained by NOESY constraints, a reminder that such methods are of limited use in the presence of large-scale dynamics.

  6. Sensitive and robust electrophoretic NMR: Instrumentation and experiments

    NASA Astrophysics Data System (ADS)

    Hallberg, Fredrik; Furó, István; Yushmanov, Pavel V.; Stilbs, Peter

    2008-05-01

    Although simple as a concept, electrophoretic NMR (eNMR) has so far failed to find wider application. Problems encountered are mainly due to disturbing and partly irreproducible convection-like bulk flow effects from both electro-osmosis and thermal convection. Additionally, bubble formation at the electrodes and rf noise pickup has constrained the typical sample geometry to U-tube-like arrangements with a small filling factor and a low resulting NMR sensitivity. Furthermore, the sign of the electrophoretic mobility cancels out in U-tube geometries. We present here a new electrophoretic sample cell based on a vertically placed conventional NMR sample tube with bubble-suppressing palladium metal as electrode material. A suitable radiofrequency filter design prevents noise pickup by the NMR sample coil from the high-voltage leads which extend into the sensitive sample volume. Hence, the obtained signal-to-noise ratio of this cell is one order of magnitude higher than that of our previous U-tube cells. Permitted by the retention of the sign of the displacement-related signal phase in the new cell design, an experimental approach is described where bulk flow effects by electro-osmosis and/or thermal convection are compensated through parallel monitoring of a reference signal from a non-charged species in the sample. This approach, together with a CPMG-like pulse train scheme provides a superior first-order cancellation of non-electrophoretic bulk flow effects.

  7. Recovering Invisible Signals by Two-Field NMR Spectroscopy.

    PubMed

    Cousin, Samuel F; Kadeřávek, Pavel; Haddou, Baptiste; Charlier, Cyril; Marquardsen, Thorsten; Tyburn, Jean-Max; Bovier, Pierre-Alain; Engelke, Frank; Maas, Werner; Bodenhausen, Geoffrey; Pelupessy, Philippe; Ferrage, Fabien

    2016-08-16

    Nuclear magnetic resonance (NMR) studies have benefited tremendously from the steady increase in the strength of magnetic fields. Spectacular improvements in both sensitivity and resolution have enabled the investigation of molecular systems of rising complexity. At very high fields, this progress may be jeopardized by line broadening, which is due to chemical exchange or relaxation by chemical shift anisotropy. In this work, we introduce a two-field NMR spectrometer designed for both excitation and observation of nuclear spins in two distinct magnetic fields in a single experiment. NMR spectra of several small molecules as well as a protein were obtained, with two dimensions acquired at vastly different magnetic fields. Resonances of exchanging groups that are broadened beyond recognition at high field can be sharpened to narrow peaks in the low-field dimension. Two-field NMR spectroscopy enables the measurement of chemical shifts at optimal fields and the study of molecular systems that suffer from internal dynamics, and opens new avenues for NMR spectroscopy at very high magnetic fields. PMID:27417269

  8. High resolution deuterium NMR studies of bacterial metabolism

    SciTech Connect

    Aguayo, J.B.; Gamcsik, M.P.; Dick, J.D.

    1988-12-25

    High resolution deuterium NMR spectra were obtained from suspensions of five bacterial strains: Escherichia coli, Clostridium perfringens, Klebsiella pneumoniae, Proteus mirabilis, and Staphylococcus aureus. Deuterium-labeled D-glucose at C-1, C-2, and C-6 was used to monitor dynamically anaerobic metabolism. The flux of glucose through the various bacterial metabolic pathways could be determined by following the disappearance of glucose and the appearance of the major end products in the 2H NMR spectrum. The presence of both labeled and unlabeled metabolites could be detected using 1H NMR spectroscopy since the proton resonances in the labeled species are shifted upfield due to an isotopic chemical shift effect. The 1H-1H scalar coupling observed in both the 2H and 1H NMR spectra was used to assign definitively the resonances of labeled species. An increase in the intensity of natural abundance deuterium signal of water can be used to monitor pathways in which a deuteron is lost from the labeled metabolite. The steps in which label loss can occur are outlined, and the influence these processes have on the ability of 2H NMR spectroscopy to monitor metabolism are assessed.

  9. Detection of thin film NMR spectrum by Magnetic Resonance Force Microscopy

    NASA Astrophysics Data System (ADS)

    Saun, Seung-Bo; Kwon, Sungmin; Lee, Soonchil; Won, Soonho

    2014-03-01

    NMR is widely used in many fields due to its powerful advantages such as nondestructive, chemically selective detection, and local probing. However, because of its low sensitivity, it is difficult to investigate thin film samples by conventional NMR. MRFM is the combined technic of NMR and Scanning Probe Microscopy (SPM), and it enabled exceptional sensitivity increasement of NMR detection. We succeeded in detecting general thin film NMR spectrum for the first time by modifying the MRFM. CaF2 34nm thin film NMR was detected and we observed 20 Gauss spectrum in proximity to bulk spectrum which is about 10 Gauss.

  10. Solid State NMR and Protein-Protein Interactions in Membranes

    PubMed Central

    Miao, Yimin; Cross, Timothy A.

    2013-01-01

    Solid state NMR spectroscopy has evolved rapidly in recent years into an excellent tool for the characterization of membrane proteins and their complexes. In the past few years it has also become clear that the structure of membrane proteins, especially helical membrane proteins is determined, in part, by the membrane environment. Therefore, the modeling of this environment by a liquid crystalline lipid bilayer for solid state NMR has generated a unique tool for the characterization of native conformational states, local and global dynamics, and high resolution structure for these proteins. Protein-protein interactions can also benefit from this solid state NMR capability to characterize membrane proteins in a native-like environment. These complexes take the form of oligomeric structures and hetero-protein interactions both with water soluble proteins and other membrane proteins. PMID:24034903

  11. Solid state NMR and protein-protein interactions in membranes.

    PubMed

    Miao, Yimin; Cross, Timothy A

    2013-12-01

    Solid state NMR spectroscopy has evolved rapidly in recent years into an excellent tool for the characterization of membrane proteins and their complexes. In the past few years it has also become clear that the structure of membrane proteins, especially helical membrane proteins is determined, in part, by the membrane environment. Therefore, the modeling of this environment by a liquid crystalline lipid bilayer for solid state NMR has generated a unique tool for the characterization of native conformational states, local and global dynamics, and high-resolution structure for these proteins. Protein-protein interactions can also benefit from this solid state NMR capability to characterize membrane proteins in a native-like environment. These complexes take the form of oligomeric structures and hetero-protein interactions both with water-soluble proteins and other membrane proteins. PMID:24034903

  12. Ligand screening by saturation-transfer difference (STD) NMR spectroscopy.

    SciTech Connect

    Krishnan, V V

    2005-04-26

    NMR based methods to screen for high-affinity ligands have become an indispensable tool for designing rationalized drugs, as these offer a combination of good experimental design of the screening process and data interpretation methods, which together provide unprecedented information on the complex nature of protein-ligand interactions. These methods rely on measuring direct changes in the spectral parameters, that are often simpler than the complex experimental procedures used to study structure and dynamics of proteins. The goal of this review article is to provide the basic details of NMR based ligand-screening methods, with particular focus on the saturation transfer difference (STD) experiment. In addition, we provide an overview of other NMR experimental methods and a practical guide on how to go about designing and implementing them.

  13. NMR imaging of cell phone radiation absorption in brain tissue

    PubMed Central

    Gultekin, David H.; Moeller, Lothar

    2013-01-01

    A method is described for measuring absorbed electromagnetic energy radiated from cell phone antennae into ex vivo brain tissue. NMR images the 3D thermal dynamics inside ex vivo bovine brain tissue and equivalent gel under exposure to power and irradiation time-varying radio frequency (RF) fields. The absorbed RF energy in brain tissue converts into Joule heat and affects the nuclear magnetic shielding and the Larmor precession. The resultant temperature increase is measured by the resonance frequency shift of hydrogen protons in brain tissue. This proposed application of NMR thermometry offers sufficient spatial and temporal resolution to characterize the hot spots from absorbed cell phone radiation in aqueous media and biological tissues. Specific absorption rate measurements averaged over 1 mg and 10 s in the brain tissue cover the total absorption volume. Reference measurements with fiber optic temperature sensors confirm the accuracy of the NMR thermometry. PMID:23248293

  14. NMRFx Processor: a cross-platform NMR data processing program.

    PubMed

    Norris, Michael; Fetler, Bayard; Marchant, Jan; Johnson, Bruce A

    2016-08-01

    NMRFx Processor is a new program for the processing of NMR data. Written in the Java programming language, NMRFx Processor is a cross-platform application and runs on Linux, Mac OS X and Windows operating systems. The application can be run in both a graphical user interface (GUI) mode and from the command line. Processing scripts are written in the Python programming language and executed so that the low-level Java commands are automatically run in parallel on computers with multiple cores or CPUs. Processing scripts can be generated automatically from the parameters of NMR experiments or interactively constructed in the GUI. A wide variety of processing operations are provided, including methods for processing of non-uniformly sampled datasets using iterative soft thresholding. The interactive GUI also enables the use of the program as an educational tool for teaching basic and advanced techniques in NMR data analysis. PMID:27457481

  15. NMR/MRI with hyperpolarized gas and high Tc SQUID

    DOEpatents

    Schlenga, Klaus; de Souza, Ricardo E.; Wong-Foy, Annjoe; Clarke, John; Pines, Alexander

    2000-01-01

    A method and apparatus for the detection of nuclear magnetic resonance (NMR) signals and production of magnetic resonance imaging (MRI) from samples combines the use of hyperpolarized inert gases to enhance the NMR signals from target nuclei in a sample and a high critical temperature (Tc) superconducting quantum interference device (SQUID) to detect the NMR signals. The system operates in static magnetic fields of 3 mT or less (down to 0.1 mT), and at temperatures from liquid nitrogen (77K) to room temperature. Sample size is limited only by the size of the magnetic field coils and not by the detector. The detector is a high Tc SQUID magnetometer designed so that the SQUID detector can be very close to the sample, which can be at room temperature.

  16. NMR and protein folding: equilibrium and stopped-flow studies.

    PubMed Central

    Frieden, C.; Hoeltzli, S. D.; Ropson, I. J.

    1993-01-01

    NMR studies are now unraveling the structure of intermediates of protein folding using hydrogen-deuterium exchange methodologies. These studies provide information about the time dependence of formation of secondary structure. They require the ability to assign specific resonances in the NMR spectra to specific amide protons of a protein followed by experiments involving competition between folding and exchange reactions. Another approach is to use 19F-substituted amino acids to follow changes in side-chain environment upon folding. Current techniques of molecular biology allow assignments of 19F resonances to specific amino acids by site-directed mutagenesis. It is possible to follow changes and to analyze results from 19F spectra in real time using a stopped-flow device incorporated into the NMR spectrometer. PMID:8298453

  17. NMR study in sodium-hydrogen-C{sub 60} superconductor

    SciTech Connect

    Ogata, H.; Miyajima, S.; Imaeda, K.; Inokuchi, H.

    1998-12-31

    {sup 23}Na and {sup 1}H NMR studies have been carried out for a Na{sub x}H{sub y}C{sub 60} superconductor. The peak position of the {sup 23}Na NMR spectrum exhibits discontinuous upfield shift of 30 ppm at about 250 K, indicates a first order phase transition. From the line shape of the {sup 23}Na spectrum obtained at 7 K, the quadrupole coupling constant tensor is evaluated to be {vert_bar}e{sup 2}Qq/h{vert_bar} = 3.7 MHz with the asymmetry parameter {eta} = 0.95. The {sup 1}H NMR spectrum suggests an anionic hydrogen state with weakly delocalized nature.

  18. Toroid cavity/coil NMR multi-detector

    DOEpatents

    Gerald, II, Rex E.; Meadows, Alexander D.; Gregar, Joseph S.; Rathke, Jerome W.

    2007-09-18

    An analytical device for rapid, non-invasive nuclear magnetic resonance (NMR) spectroscopy of multiple samples using a single spectrometer is provided. A modified toroid cavity/coil detector (TCD), and methods for conducting the simultaneous acquisition of NMR data for multiple samples including a protocol for testing NMR multi-detectors are provided. One embodiment includes a plurality of LC resonant circuits including spatially separated toroid coil inductors, each toroid coil inductor enveloping its corresponding sample volume, and tuned to resonate at a predefined frequency using a variable capacitor. The toroid coil is formed into a loop, where both ends of the toroid coil are brought into coincidence. Another embodiment includes multiple micro Helmholtz coils arranged on a circular perimeter concentric with a central conductor of the toroid cavity.

  19. Remote NMR/MRI detection of laser polarized gases

    DOEpatents

    Pines, Alexander; Saxena, Sunil; Moule, Adam; Spence, Megan; Seeley, Juliette A.; Pierce, Kimberly L.; Han, Song-I; Granwehr, Josef

    2006-06-13

    An apparatus and method for remote NMR/MRI spectroscopy having an encoding coil with a sample chamber, a supply of signal carriers, preferably hyperpolarized xenon and a detector allowing the spatial and temporal separation of signal preparation and signal detection steps. This separation allows the physical conditions and methods of the encoding and detection steps to be optimized independently. The encoding of the carrier molecules may take place in a high or a low magnetic field and conventional NMR pulse sequences can be split between encoding and detection steps. In one embodiment, the detector is a high magnetic field NMR apparatus. In another embodiment, the detector is a superconducting quantum interference device. A further embodiment uses optical detection of Rb--Xe spin exchange. Another embodiment uses an optical magnetometer using non-linear Faraday rotation. Concentration of the signal carriers in the detector can greatly improve the signal to noise ratio.

  20. A simple low-cost single-crystal NMR setup.

    PubMed

    Vinding, Mads S; Kessler, Tommy O; Vosegaard, Thomas

    2016-08-01

    A low-cost single-crystal NMR kit is presented along with a web-based post-processing software. The kit consists of a piezo-crystal motor and a goniometer for the crystal, both embedded in a standard wide-bore NMR probe with a 3D printed scaffold. The NMR pulse program controls the angle setting automatically, and the post-processing software incorporates a range of orientation-angle discrepancies present in the kit and other single-crystal setups. Results with a NaNO3 single-crystal show a high degree of reproducibility and excellent agreement with previous findings for the anisotropic quadrupolar interaction. PMID:27295612

  1. Mobile sensor for high resolution NMR spectroscopy and imaging

    NASA Astrophysics Data System (ADS)

    Danieli, Ernesto; Mauler, Jörg; Perlo, Juan; Blümich, Bernhard; Casanova, Federico

    2009-05-01

    In this work we describe the construction of a mobile NMR tomograph with a highly homogeneous magnetic field. Fast MRI techniques as well as NMR spectroscopy measurements were carried out. The magnet is based on a Halbach array built from identical permanent magnet blocks generating a magnetic field of 0.22 T. To shim the field inhomogeneities inherent to magnet arrays constructed from these materials, a shim strategy based on the use of movable magnet blocks is employed. With this approach a reduction of the line-width from ˜20 kHz to less than 0.1 kHz was achieved, that is by more than two orders of magnitude, in a volume of 21 cm 3. Implementing a RARE sequence, 3D images of different objects placed in this volume were obtained in short experimental times. Moreover, by reducing the sample size to 1 cm 3, sub ppm resolution is obtained in 1H NMR spectra.

  2. In-Cell Protein Structures from 2D NMR Experiments.

    PubMed

    Müntener, Thomas; Häussinger, Daniel; Selenko, Philipp; Theillet, Francois-Xavier

    2016-07-21

    In-cell NMR spectroscopy provides atomic resolution insights into the structural properties of proteins in cells, but it is rarely used to solve entire protein structures de novo. Here, we introduce a paramagnetic lanthanide-tag to simultaneously measure protein pseudocontact shifts (PCSs) and residual dipolar couplings (RDCs) to be used as input for structure calculation routines within the Rosetta program. We employ this approach to determine the structure of the protein G B1 domain (GB1) in intact Xenopus laevis oocytes from a single set of 2D in-cell NMR experiments. Specifically, we derive well-defined GB1 ensembles from low concentration in-cell NMR samples (∼50 μM) measured at moderate magnetic field strengths (600 MHz), thus offering an easily accessible alternative for determining intracellular protein structures. PMID:27379949

  3. RNA structure determination by solid-state NMR spectroscopy

    PubMed Central

    Marchanka, Alexander; Simon, Bernd; Althoff-Ospelt, Gerhard; Carlomagno, Teresa

    2015-01-01

    Knowledge of the RNA three-dimensional structure, either in isolation or as part of RNP complexes, is fundamental to understand the mechanism of numerous cellular processes. Because of its flexibility, RNA represents a challenge for crystallization, while the large size of cellular complexes brings solution-state NMR to its limits. Here, we demonstrate an alternative approach on the basis of solid-state NMR spectroscopy. We develop a suite of experiments and RNA labeling schemes and demonstrate for the first time that ssNMR can yield a RNA structure at high-resolution. This methodology allows structural analysis of segmentally labelled RNA stretches in high-molecular weight cellular machines—independent of their ability to crystallize— and opens the way to mechanistic studies of currently difficult-to-access RNA-protein assemblies. PMID:25960310

  4. Computer systems for laboratory networks and high-performance NMR.

    PubMed

    Levy, G C; Begemann, J H

    1985-08-01

    Modern computer technology is significantly enhancing the associated tasks of spectroscopic data acquisition and data reduction and analysis. Distributed data processing techniques, particularly laboratory computer networking, are rapidly changing the scientist's ability to optimize results from complex experiments. Optimization of nuclear magnetic resonance spectroscopy (NMR) and magnetic resonance imaging (MRI) experimental results requires use of powerful, large-memory (virtual memory preferred) computers with integrated (and supported) high-speed links to magnetic resonance instrumentation. Laboratory architectures with larger computers, in order to extend data reduction capabilities, have facilitated the transition to NMR laboratory computer networking. Examples of a polymer microstructure analysis and in vivo 31P metabolic analysis are given. This paper also discusses laboratory data processing trends anticipated over the next 5-10 years. Full networking of NMR laboratories is just now becoming a reality. PMID:3840171

  5. Deuterium NMR Studies of the Structure and Dynamics of Gramicidin.

    NASA Astrophysics Data System (ADS)

    Hing, Andrew William

    1990-01-01

    The structure and dynamics of the membrane peptide gramicidin are investigated by deuterium NMR. A specific structural and dynamical question about the peptide backbone of gramicidin is investigated by deuterating the alpha carbon of the third alanine residue. Deuterium NMR experiments performed on this analog in oriented lipid bilayers indicate that the c_alpha- ^2H bond makes an angle relative to the helical axis that is in agreement with the bond angle predicted by the beta^{6.3} helical model. A second structural and dynamical question about the peptide backbone of gramicidin is investigated by deuterating the formyl group of two different analogs. Deuterium NMR experiments performed on these analogs show that the spectra of the two analogs are very similar. However, the analog possessing D-leucine as the second residue also appears to exist in a second, minor conformation which does not seem to exist for the analog possessing glycine as the second residue.

  6. An on-line NMR technique with a programmable processor

    SciTech Connect

    Razazian, K.; Dieckman, S.L.; Raptis, A.C.

    1995-07-01

    Nuclear magnetic resonance (NMR) spectroscopy is used to determine molecular content of materials, mainly in laboratory measurements. The reduced cost of fast computer processors, together with recent break throughs in digital signal processor technology, has facilitated the on-line use of NMR by allowing modifications of the available technology. This paper describes a system and an algorithm for improving the on-line operations. It is base on the time-domain NMR signal detected by the controller and some prior knowledge of chemical signal patterns. The desired signal can be separated from a composite signal by using an adaptive line enhancer (ALE) filter. This technique would be useful for upgrading process procedures in on-line manufacturing.

  7. Paramagnetic shimming for wide-range variable-field NMR.

    PubMed

    Ichijo, Naoki; Takeda, Kazuyuki; Takegoshi, K

    2014-09-01

    We propose a new passive shimming strategy for variable-field NMR experiments, in which the magnetic field produced by paramagnetic shim pieces placed inside the magnet bore compensates the inhomogeneity of a variable-field magnet for a wide range of magnet currents. Paramagnetic shimming is demonstrated in (7)Li, (87)Rb, and (45)Sc NMR of a liquid solution sample in magnetic fields of 3.4, 4.0, and 5.4T at a fixed carrier frequency of 56.0MHz. Since both the main-field inhomogeneity and the paramagnetic magnetization are proportional to the main-magnet current, the resonance lines are equally narrowed by the improved field homogeneity with an identical configuration of the paramagnetic shim pieces. Paramagnetic shimming presented in this work opens the possibility of high-resolution variable-field NMR experiments. PMID:25080372

  8. Software-assisted serum metabolite quantification using NMR.

    PubMed

    Jung, Young-Sang; Hyeon, Jin-Seong; Hwang, Geum-Sook

    2016-08-31

    The goal of metabolomics is to analyze a whole metabolome under a given set of conditions, and accurate and reliable quantitation of metabolites is crucial. Absolute concentration is more valuable than relative concentration; however, the most commonly used method in NMR-based serum metabolic profiling, bin-based and full data point peak quantification, provides relative concentration levels of metabolites and are not reliable when metabolite peaks overlap in a spectrum. In this study, we present the software-assisted serum metabolite quantification (SASMeQ) method, which allows us to identify and quantify metabolites in NMR spectra using Chenomx software. This software uses the ERETIC2 utility from TopSpin to add a digitally synthesized peak to a spectrum. The SASMeQ method will advance NMR-based serum metabolic profiling by providing an accurate and reliable method for absolute quantification that is superior to bin-based quantification. PMID:27506360

  9. High Pressure NMR Methods for Characterizing Functional Substates of Proteins.

    PubMed

    Kalbitzer, Hans Robert

    2015-01-01

    Proteins usually exist in multiple conformational states in solution. High pressure NMR spectroscopy is a well-suited method to identify these states. In addition, these states can be characterized by their thermodynamic parameters, the free enthalpies at ambient pressure, the partial molar volumes, and the partial molar compressibility that can be obtained from the analysis of the high pressure NMR data. Two main types of states of proteins exist, functional states and folding states. There is a strong link between these two types, the functional states represent essential folding states (intermediates), other folding states may have no functional meaning (optional folding states). In this chapter, this concept is tested on the Ras protein, an important proto-oncogen in humans where all substates required by theory can be identified experimentally by high pressure NMR spectroscopy. Finally, we show how these data can be used to develop allosteric inhibitors of proteins. PMID:26174382

  10. NMR characteristics in noncentrosymmetric Mo3Al2C

    NASA Astrophysics Data System (ADS)

    Kuo, C. N.; Liu, H. F.; Lue, C. S.

    2012-02-01

    We present an extensive study of the noncentrosymmetric superconductor Mo3Al2C using 27Al nuclear magnetic resonance (NMR) spectroscopy. The NMR line shapes, Knight shifts, as well as spin-lattice relaxation rates in both superconducting and normal states have been identified. In the superconducting phase, the results of the Knight shift and relaxation rate signify the existence of finite density of states, attributed to the strong antisymmetric spin-orbital coupling effect enhanced by intrinsic defects. In the normal state, peculiar changes such as the broadening of the NMR linewidth and the distinct drop of the Knight shift were discerned across a characteristic temperature of T*≃196 K. Moreover, the magnitude of 1/T1T decreases markedly and develops pseudogaplike behavior below T*. We associated these anomalous features with distortions near the Al sites toward a lower symmetric structural environment, leading to the modification of electronic structures around Fermi surfaces.

  11. NMR structure improvement: A structural bioinformatics & visualization approach

    NASA Astrophysics Data System (ADS)

    Block, Jeremy N.

    The overall goal of this project is to enhance the physical accuracy of individual models in macromolecular NMR (Nuclear Magnetic Resonance) structures and the realism of variation within NMR ensembles of models, while improving agreement with the experimental data. A secondary overall goal is to combine synergistically the best aspects of NMR and crystallographic methodologies to better illuminate the underlying joint molecular reality. This is accomplished by using the powerful method of all-atom contact analysis (describing detailed sterics between atoms, including hydrogens); new graphical representations and interactive tools in 3D and virtual reality; and structural bioinformatics approaches to the expanded and enhanced data now available. The resulting better descriptions of macromolecular structure and its dynamic variation enhances the effectiveness of the many biomedical applications that depend on detailed molecular structure, such as mutational analysis, homology modeling, molecular simulations, protein design, and drug design.

  12. NMR imaging of cell phone radiation absorption in brain tissue.

    PubMed

    Gultekin, David H; Moeller, Lothar

    2013-01-01

    A method is described for measuring absorbed electromagnetic energy radiated from cell phone antennae into ex vivo brain tissue. NMR images the 3D thermal dynamics inside ex vivo bovine brain tissue and equivalent gel under exposure to power and irradiation time-varying radio frequency (RF) fields. The absorbed RF energy in brain tissue converts into Joule heat and affects the nuclear magnetic shielding and the Larmor precession. The resultant temperature increase is measured by the resonance frequency shift of hydrogen protons in brain tissue. This proposed application of NMR thermometry offers sufficient spatial and temporal resolution to characterize the hot spots from absorbed cell phone radiation in aqueous media and biological tissues. Specific absorption rate measurements averaged over 1 mg and 10 s in the brain tissue cover the total absorption volume. Reference measurements with fiber optic temperature sensors confirm the accuracy of the NMR thermometry. PMID:23248293

  13. High resolution NMR measurements using a 400 MHz NMR with an (RE)Ba2Cu3O7-x high-temperature superconducting inner coil: Towards a compact super-high-field NMR

    NASA Astrophysics Data System (ADS)

    Piao, R.; Iguchi, S.; Hamada, M.; Matsumoto, S.; Suematsu, H.; Saito, A. T.; Li, J.; Nakagome, H.; Takao, T.; Takahashi, M.; Maeda, H.; Yanagisawa, Y.

    2016-02-01

    Use of high-temperature superconducting (HTS) inner coils in combination with conventional low-temperature superconducting (LTS) outer coils for an NMR magnet, i.e. a LTS/HTS NMR magnet, is a suitable option to realize a high-resolution NMR spectrometer with operating frequency >1 GHz. From the standpoint of creating a compact magnet, (RE: Rare earth) Ba2Cu3O7-x (REBCO) HTS inner coils which can tolerate a strong hoop stress caused by a Lorentz force are preferred. However, in our previous work on a first-generation 400 MHz LTS/REBCO NMR magnet, the NMR resolution and sensitivity were about ten times worse than that of a conventional LTS NMR magnet. The result was caused by a large field inhomogeneity in the REBCO coil itself and the shielding effect of a screening current induced in that coil. In the present paper, we describe the operation of a modified 400 MHz LTS/REBCO NMR magnet with an advanced field compensation technology using a combination of novel ferromagnetic shimming and an appropriate procedure for NMR spectrum line shape optimization. We succeeded in obtaining a good NMR line shape and 2D NOESY spectrum for a lysozyme aqueous sample. We believe that this technology is indispensable for the realization of a compact super-high-field high-resolution NMR.

  14. Quantitating Metabolites in Protein Precipitated Serum Using NMR Spectroscopy

    PubMed Central

    2015-01-01

    Quantitative NMR-based metabolite profiling is challenged by the deleterious effects of abundant proteins in the intact blood plasma/serum, which underscores the need for alternative approaches. Protein removal by ultrafiltration using low molecular weight cutoff filters thus represents an important step. However, protein precipitation, an alternative and simple approach for protein removal, lacks detailed quantitative assessment for use in NMR based metabolomics. In this study, we have comprehensively evaluated the performance of protein precipitation using methanol, acetonitrile, perchloric acid, and trichloroacetic acid and ultrafiltration approaches using 1D and 2D NMR, based on the identification and absolute quantitation of 44 human blood metabolites, including a few identified for the first time in the NMR spectra of human serum. We also investigated the use of a “smart isotope tag,” 15N-cholamine for further resolution enhancement, which resulted in the detection of a number of additional metabolites. 1H NMR of both protein precipitated and ultrafiltered serum detected all 44 metabolites with comparable reproducibility (average CV, 3.7% for precipitation; 3.6% for filtration). However, nearly half of the quantified metabolites in ultrafiltered serum exhibited 10–74% lower concentrations; specifically, tryptophan, benzoate, and 2-oxoisocaproate showed much lower concentrations compared to protein precipitated serum. These results indicate that protein precipitation using methanol offers a reliable approach for routine NMR-based metabolomics of human blood serum/plasma and should be considered as an alternative to ultrafiltration. Importantly, protein precipitation, which is commonly used by mass spectrometry (MS), promises avenues for direct comparison and correlation of metabolite data obtained from the two analytical platforms to exploit their combined strength in the metabolomics of blood. PMID:24796490

  15. NMR imaging of fluid dynamics in reservoir core.

    PubMed

    Baldwin, B A; Yamanashi, W S

    1988-01-01

    A medical NMR imaging instrument has been modified to image water and oil in reservoir rocks by the construction of a new receiving coil. Both oil and water inside the core produced readily detectable proton NMR signals, while the rock matrix produced no signal. Because of similar T2 NMR relaxation times, the water was doped with a paramagnetic ion, Mn+2, to reduce its T2 relaxation time. This procedure enhanced the separation between the oil and water phases in the resulting images. Sequential measurements, as water imbibed into one end and oil was expelled from the other end of a core plug, produced a series of images which showed the dynamics of the fluids. For water-wet Berea Sandstone a flood front was readily observed, but some of the oil was apparently left behind in small, isolated pockets which were larger than individual pores. After several additional pore volumes of water flowed through the plug the NMR image indicated a homogeneous distribution of oil. The amount of residual oil, as determined from the ratio of NMR intensities, closely approximated the residual oil saturation of fully flooded Berea samples measured by Dean-Stark extraction. A Berea sandstone core treated to make it partially oil-wet, did not show a definitive flood front, but appeared to channel the water around the perimeter of the core plug. The relative ease with which these images were made indicates that NMR imaging can be a useful technique to follow the dynamics of oil and water through a core plug for a variety of production processes. PMID:3226235

  16. NMR study of compressed supercritical water

    NASA Astrophysics Data System (ADS)

    Lamb, W. J.; Jonas, J.

    1981-01-01

    The proton spin-lattice relaxation time T1 in water has been measured as a function of pressure in the temperature range 150 to 700°C. This study focuses on the supercritical region (tc=374°C) where the spin-rotation interaction mechanism dominates the observed proton relaxation rate. Since water is an asymmetric top molecule, the analysis of the experimental data involves a number of simplifying assumptions discussed in detail. The experimental finding that in supercritical water the spin-rotation relaxation time T 1SR is a linear function of density ρ, up to relatively high densities (ρ≃ 1.5 ρc) provides rationale for analysis of the NMR experimental data in terms of a model used for dilute gases. The T 1SR data are analyzed on the basis of the assumption that the collision modulated spin-rotation interactions can be described by a single correlation function which is an exponential function of time. Using this procedure, we find that T 1SR/ρ αT-2, i.e.T 1SR/ρ exhibits a stronger temperature dependence than that found (T 1SR/ρ αT-3/2) for many polar and nonpolar gases. The calculated effective cross sections for the transfer of angular momentum σeff which show strong temperature dependence (σeff αT-1.5) are several times larger than the kinetic cross sections. By assuming applicability of expressions derived for isotropic reorientation of spherical-top molecules and using the effective spin-rotation interaction constant as obtained from microwave measurements, we are able to calculate the angular momentum correlation time τJ, over the range of temperatures and densities studied. In the supercritical region τJ⩾τΘ, where τΘ is the reorientational correlation time, and the estimated mean angle of reorientation ΔΘ¯ is in the range 50° to 800°. The T 1SR data are also interpreted in terms of the modified rough hard sphere (RHS) model which for ρ<2ρc takes into account the effect of attractive forces. We find that 1/T 1SR is a linear

  17. Experimental demonstration of quantum contextuality on an NMR qutrit

    NASA Astrophysics Data System (ADS)

    Dogra, Shruti; Dorai, Kavita; Arvind

    2016-05-01

    We experimentally test quantum contextuality of a single qutrit using NMR. The contextuality inequalities based on nine observables developed by Kurzynski et al. are first reformulated in terms of traceless observables which can be measured in an NMR experiment. These inequalities reveal the contextuality of almost all single-qutrit states. We demonstrate the violation of the inequality on four different initial states of a spin-1 deuterium nucleus oriented in a liquid crystal matrix, and follow the violation as the states evolve in time. We also describe and experimentally perform a single-shot test of contextuality for a subclass of qutrit states whose density matrix is diagonal in the energy basis.

  18. Sensitivity Enhancement in Solution NMR: Emerging Ideas and New Frontiers

    PubMed Central

    Lee, Jung Ho; Okuno, Yusuke; Cavagnero, Silvia

    2014-01-01

    Modern NMR spectroscopy has reached an unprecedented level of sophistication in the determination of biomolecular structure and dynamics at atomic resolution in liquids. However, the sensitivity of this technique is still too low to solve a variety of cutting-edge biological problems in solution, especially those that involve viscous samples, very large biomolecules or aggregation-prone systems that need to be kept at low concentration. Despite the challenges, a variety of efforts have been carried out over the years to increase sensitivity of NMR spectroscopy in liquids. This review discusses basic concepts, recent developments and future opportunities in this exciting area of research. PMID:24656077

  19. Some specific features of the NMR study of fluid flows

    NASA Astrophysics Data System (ADS)

    Davydov, V. V.

    2016-07-01

    Some specific features of studying fluid flows with a NMR spectrometer are considered. The consideration of these features in the NMR spectrometer design makes it possible to determine the relative concentrations of paramagnetic ions and measure the longitudinal and transverse relaxation times ( T 1 and T 2, respectively) in fluid flows with an error no larger than 0.5%. This approach allows one to completely avoid errors in determining the state of a fluid from measured relaxation constants T 1 and T 2, which is especially urgent when working with medical suspensions and biological solutions. The results of an experimental study of fluid flows are presented.

  20. Instrument Control and Data Acquisition for NMR Experiments

    Energy Science and Technology Software Center (ESTSC)

    1999-03-29

    This is a software program which is intended to do some instrument control and data acquisition for NMR experiments. The basic purpose of the program is to allow a user of the NMR system to create a list of instructions which tells the program what steps should be done, the stat the data taking program and let the system run by itself (depending on the type of sample and the type of experiment being run,more » it can take from several minutes to many hours to do a data collection run).« less

  1. Applications of NMR in the characterization of pharmaceutical microemulsions.

    PubMed

    Hathout, Rania M; Woodman, Timothy J

    2012-07-10

    Microemulsions have successfully proven themselves as useful vehicles for drugs through the different routes of administration because they can confer on drugs greater water solubility and bioavailability. The ability to understand the structural aspects of these important drug delivery systems is essential to the progress of this science. The use of NMR techniques in pharmaceutical and drug delivery science is increasing especially in the characterization field. This review demonstrates the major and novel NMR methods and techniques used in understanding and characterizing the different microemulsion components, types and structures. PMID:22579644

  2. MAS PFG NMR Studies of Mixtures in Porous Materials

    NASA Astrophysics Data System (ADS)

    Gratz, Marcel; Hertel, Stefan; Wehring, Markus; Schlayer, Stefan; Stallmach, Frank; Galvosas, Petrik

    2011-03-01

    Pulsed field gradient (PFG) and magic angle spinning (MAS) NMR techniques have been successfully combined for the study of mixture diffusion in porous materials. Using a modular setup of commercially available components, gradient pulses of up to ±2.6 T/m can be applied coinciding with fast sample rotation at the magic angle. Methods for the proper alignment of all components are presented along with protocols for MAS PFG NMR experiments. Finally, first diffusion measurements of n-hexane and benzene being adsorbed together in the metal-organic framework MOF-5 are presented.

  3. On the solid-state NMR spectra of naproxen

    NASA Astrophysics Data System (ADS)

    Czernek, Jiří

    2015-01-01

    Two previous measurements of the 13C and 1H NMR isotropic chemical shifts in crystalline naproxen, which is an important pharmaceutical compound, are confronted with the results obtained from several theoretical approaches capable of the proper treatment of solid-phase effects. In the underlying geometrical optimizations, two crystal structures are considered. The agreement between the data sets is quantified, including an evaluation of the similarity between the experimental solid-state NMR spectra. The 13C-1H heteronuclear correlations are analyzed, and their various assignments are discussed employing the statistical treatment of the differences between the measured and theoretical isotropic chemical shifts.

  4. NMR Meets Tau: Insights into Its Function and Pathology

    PubMed Central

    Lippens, Guy; Landrieu, Isabelle; Smet, Caroline; Huvent, Isabelle; Gandhi, Neha S.; Gigant, Benoît; Despres, Clément; Qi, Haoling; Lopez, Juan

    2016-01-01

    In this review, we focus on what we have learned from Nuclear Magnetic Resonance (NMR) studies on the neuronal microtubule-associated protein Tau. We consider both the mechanistic details of Tau: the tubulin relationship and its aggregation process. Phosphorylation of Tau is intimately linked to both aspects. NMR spectroscopy has depicted accurate phosphorylation patterns by different kinases, and its non-destructive character has allowed functional assays with the same samples. Finally, we will discuss other post-translational modifications of Tau and its interaction with other cellular factors in relationship to its (dys)function. PMID:27338491

  5. MVAPACK: A Complete Data Handling Package for NMR Metabolomics

    PubMed Central

    2015-01-01

    Data handling in the field of NMR metabolomics has historically been reliant on either in-house mathematical routines or long chains of expensive commercial software. Thus, while the relatively simple biochemical protocols of metabolomics maintain a low barrier to entry, new practitioners of metabolomics experiments are forced to either purchase expensive software packages or craft their own data handling solutions from scratch. This inevitably complicates the standardization and communication of data handling protocols in the field. We report a newly developed open-source platform for complete NMR metabolomics data handling, MVAPACK, and describe its application on an example metabolic fingerprinting data set. PMID:24576144

  6. Advanced NMR approaches in the characterization of coal

    SciTech Connect

    Maciel, G.E.

    1992-01-01

    A considerable effort in this project during the past few months has been focussed on the development of [sup 1]H and [sup 13]C NMR imaging techniques to yield spatially-resolved chemical shift (structure) information on coal. In order to yield the chemical shift information, a solid-state NMR imaging technique must include magic-angle spinning, so rotating gradient capabilities are indicated. A [sup 13]C MAS imaging probe and a [sup 1]H MAS imaging probe and the circuitry necessary for rotating gradients have been designed and constructed. The [sup 1]H system has already produced promising preliminary results, which are briefly described in this report.

  7. Overview on the use of NMR to examine protein structure.

    PubMed

    Breukels, Vincent; Konijnenberg, Albert; Nabuurs, Sanne M; Doreleijers, Jurgen F; Kovalevskaya, Nadezda V; Vuister, Geerten W

    2011-04-01

    Any protein structure determination process contains several steps, starting from obtaining a suitable sample, then moving on to acquiring data and spectral assignment, and lastly to the final steps of structure determination and validation. This unit describes all of these steps, starting with the basic physical principles behind NMR and some of the most commonly measured and observed phenomena such as chemical shift, scalar and residual coupling, and the nuclear Overhauser effect. Then, in somewhat more detail, the process of spectral assignment and structure elucidation is explained. Furthermore, the use of NMR to study protein-ligand interaction, protein dynamics, or protein folding is described. PMID:21488042

  8. Localized double-quantum-filtered 1H NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Thomas, M. A.; Hetherington, H. P.; Meyerhoff, D. J.; Twieg, D. B.

    The image-guided in vivo spectroscopic (ISIS) pulse sequence has been combined with a double-quantum-filter scheme in order to obtain localized and water-suppressed 1H NMR spectra of J-coupled metabolites. The coherence-transfer efficiency associated with the DQ filter for AX and A 3X spin systems is described. Phantom results of carnosine, alanine, and ethanol in aqueous solution are presented. For comparison, the 1H NMR spectrum of alanine in aqueous solution with the binomial (1331, 2662) spin-echo sequence is also shown.

  9. In situ NMR analysis of fluids contained in sedimentary rock

    PubMed

    de Swiet TM; Tomaselli; Hurlimann; Pines

    1998-08-01

    Limitations of resolution and absorption in standard chemical spectroscopic techniques have made it difficult to study fluids in sedimentary rocks. In this paper, we show that a chemical characterization of pore fluids may be obtained in situ by magic angle spinning (MAS) nuclear magnetic resonance (NMR), which is normally used for solid samples. 1H MAS-NMR spectra of water and crude oil in Berea sandstone show sufficient chemical shift resolution for a straightforward determination of the oil/water ratio. Copyright 1998 Academic Press. PMID:9716484

  10. NMR Meets Tau: Insights into Its Function and Pathology.

    PubMed

    Lippens, Guy; Landrieu, Isabelle; Smet, Caroline; Huvent, Isabelle; Gandhi, Neha S; Gigant, Benoît; Despres, Clément; Qi, Haoling; Lopez, Juan

    2016-01-01

    In this review, we focus on what we have learned from Nuclear Magnetic Resonance (NMR) studies on the neuronal microtubule-associated protein Tau. We consider both the mechanistic details of Tau: the tubulin relationship and its aggregation process. Phosphorylation of Tau is intimately linked to both aspects. NMR spectroscopy has depicted accurate phosphorylation patterns by different kinases, and its non-destructive character has allowed functional assays with the same samples. Finally, we will discuss other post-translational modifications of Tau and its interaction with other cellular factors in relationship to its (dys)function. PMID:27338491

  11. Assigning the NMR Spectrum of Glycidol: An Advanced Organic Chemistry Exercise

    ERIC Educational Resources Information Center

    Helms, Eric; Arpaia, Nicholas; Widener, Melissa

    2007-01-01

    Various one- and two-dimensional NMR experiments have been found to be extremely useful for assigning the proton and carbon NMR spectra of glycidol. The technique provides extremely valuable information aiding in the complete assignment of the peaks.

  12. COMPREHENSIVE PROGRESS REPORT FOR FOURIER TRANSFORM NMR (NUCLEAR MAGNETIC RESONANCE) OF METALS OF ENVIRONMENTAL SIGNIFICANCE

    EPA Science Inventory

    Interactions of the metals cadmium and selenium with various biologically important substrates were studied by nuclear magnetic resonance (NMR) spectroscopy. Cadmium-113 NMR was used for a critical examination of three metalloproteins: concanavalin A, bovine superoxide dismutase ...

  13. LC-NMR Technique in the Analysis of Phytosterols in Natural Extracts.

    PubMed

    Horník, Stěpán; Sajfrtová, Marie; Karban, Jindřich; Sýkora, Jan; Březinová, Anna; Wimmer, Zdeněk

    2013-01-01

    The ability of LC-NMR to detect simultaneously free and conjugated phytosterols in natural extracts was tested. The advantages and disadvantages of a gradient HPLC-NMR method were compared to the fast composition screening using SEC-NMR method. Fractions of free and conjugated phytosterols were isolated and analyzed by isocratic HPLC-NMR methods. The results of qualitative and quantitative analyses were in a good agreement with the literature data. PMID:24455424

  14. Statistical models and NMR analysis of polymer microstructure

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Statistical models can be used in conjunction with NMR spectroscopy to study polymer microstructure and polymerization mechanisms. Thus, Bernoullian, Markovian, and enantiomorphic-site models are well known. Many additional models have been formulated over the years for additional situations. Typica...

  15. Relative Configuration of Natural Products Using NMR Chemical Shifts

    Technology Transfer Automated Retrieval System (TEKTRAN)

    By comparing calculated with experimental NMR chemical shifts, we were able to determine the relative configurations of three monoterpene diastereomers produced by the walkingstick Anisomorpha buprestoides. The combined RMSDs of both 1H and 13C quantum chemically calculated shifts were able to predi...

  16. NMR Structures of Membrane Proteins in Phospholipid Bilayers

    PubMed Central

    Radoicic, Jasmina; Lu, George J.; Opella, Stanley J.

    2014-01-01

    Membrane proteins have always presented technical challenges for structural studies because of their requirement for a lipid environment. Multiple approaches exist including X-ray crystallography and electron microscopy that can give significant insights into their structure and function. However, nuclear magnetic resonance (NMR) is unique in that it offers the possibility of determining the structures of unmodified membrane proteins in their native environment of phospholipid bilayers under physiological conditions. Furthermore, NMR enables the characterization of the structure and dynamics of backbone and side chain sites of the proteins alone and in complexes with both small molecules and other biopolymers. The learning curve has been steep for the field as most initial studies were performed under non-native environments using modified proteins until ultimately progress in both techniques and instrumentation led to the possibility of examining unmodified membrane proteins in phospholipid bilayers under physiological conditions. This review aims to provide an overview of the development and application of NMR to membrane proteins. It highlights some of the most significant structural milestones that have been reached by NMR spectroscopy of membrane proteins; especially those accomplished with the proteins in phospholipid bilayer environments where they function. PMID:25032938

  17. Quantitative evaluation of porous media wettability using NMR relaxometry.

    PubMed

    Fleury, M; Deflandre, F

    2003-01-01

    We propose a new method to determine wettability indices from NMR relaxometry. The new method uses the sensitivity of low field NMR relaxometry to the fluid distribution in oil-water saturated porous media. The model is based on the existence of a surface relaxivity for both oil and water, allowing the determination of the amount of surface wetted either by oil or by water. The proposed NMR wettability index requires the measurement of relaxation time distribution at four different saturation states. At the irreducible water saturation, we determine the dominant relaxation time of oil in the presence of a small amount of water, and at the oil residual saturation, we determine the dominant relaxation time of water in the presence of a small amount of oil. At 100% water and 100% oil saturation, we determine the surface relaxivity ratio. The interaction of oil with the surface is also evidenced by the comparison of the spin-lattice (T1) and spin-locking (T1rho) relaxation times. The new NMR index agrees with standard wettability measurements based on drainage-imbibition capillary pressure curves (USBM test) in the range [-0.3-1]. PMID:12850740

  18. Protein structure by solid-state NMR of oriented systems

    SciTech Connect

    Stewart, P.L.

    1987-01-01

    A method for determining protein backbone structure from angular information obtainable by solid state NMR spectroscopy is presented. Various spin interactions including quadrupole, dipole, and chemical shift interactions and nuclei including /sup 14/N, /sup 15/N, /sup 13/C, and /sup 2/H may be observed. Angularly dependent measurements can be made when the sample has at least one direction of order along the externally applied magnetic field. Several NMR parameters are used to determine the orientation of each peptide plane with respect to the magnetic field vector, B/sub O/, to within a few symmetry related possibilities. The computer program Totlink can then be used to perform the necessary coordinate transformations and to evaluate the possible backbone structures and select for the most chemically reasonable. Experimental /sup 14/N NMR structural studies of the model peptides n-acetyl-d,l-valine, n-acetyl-l-valyl-l-leucine, and l-alanyl-glycyl-glycine and preliminary /sup 14/N NMR results on a large single crystal of orthorhombic lysozyme are presented.

  19. Amplification of Xenon NMR and MRI by remote detection

    SciTech Connect

    Moule, Adam J.; Spence, Megan M.; Han, Song-I.; Seeley, JulietteA.; Pierce, Kimberly L.; Saxena, Sunil; Pines, Alexander

    2003-03-31

    A novel technique is proposed in which a nuclear magneticresonance (NMR) spectrum or magnetic resonance image (MRI) is encoded andstored as spin polarization and is then moved to a different physicallocation to be detected. Remote detection allows the separateoptimization of the encoding and detection steps, permitting theindependent choice of experimental conditions, and excitation anddetection methodologies. In the first experimental demonstration of thistechnique, we show that NMR signal can be amplified by taking diluted129Xe from a porous sample placed inside a large encoding coil, andconcentrating it into a smaller detection coil. In general, the study ofNMR active molecules at low concentration that have low physical fillingfactor is facilitated by remote detection. In the second experiment, MRIinformation encoded in a very low field magnet (4-7mT) is transferred toa high field magnet (4.2 T) in order to be detected under optimizedconditions. Furthermore, remote detection allows the utilization ofultra-sensitive optical or superconducting detection techniques, whichbroadens the horizon of NMR experimentation.

  20. NMR method for accurate quantification of polysorbate 80 copolymer composition.

    PubMed

    Zhang, Qi; Wang, Aifa; Meng, Yang; Ning, Tingting; Yang, Huaxin; Ding, Lixia; Xiao, Xinyue; Li, Xiaodong

    2015-10-01

    (13)C NMR spectroscopic integration employing short relaxation delays and a 30° pulse width was evaluated as a quantitative tool for analyzing the components of polysorbate 80. (13)C NMR analysis revealed that commercial polysorbate 80 formulations are a complex oligomeric mixture of sorbitan polyethoxylate esters and other intermediates, such as isosorbide polyethoxylate esters and poly(ethylene glycol) (PEG) esters. This novel approach facilitates the quantification of the component ratios. In this study, the ratios of the three major oligomers in polysorbate 80 were measured and the PEG series was found to be the major component of commercial polysorbate 80. The degree of polymerization of -CH2CH2O- groups and the ratio of free to bonded -CH2CH2O- end groups, which correlate with the hydrophilic/hydrophobic nature of the polymer, were analyzed, and were suggested to be key factors for assessing the likelihood of adverse biological reactions to polysorbate 80. The (13)C NMR data suggest that the feed ratio of raw materials and reaction conditions in the production of polysorbate 80 are not well controlled. Our results demonstrate that (13)C NMR is a universal, powerful tool for polysorbate analysis. Such analysis is crucial for the synthesis of a high-quality product, and is difficult to obtain by other methods. PMID:26356097

  1. 103Rh NMR spectroscopy and its application to rhodium chemistry.

    PubMed

    Ernsting, Jan Meine; Gaemers, Sander; Elsevier, Cornelis J

    2004-09-01

    Rhodium is used for a number of large processes that rely on homogeneous rhodium-catalyzed reactions, for instance rhodium-catalyzed hydroformylation of alkenes, carbonylation of methanol to acetic acid and hydrodesulfurization of thiophene derivatives (in crude oil). Many laboratory applications in organometallic chemistry and catalysis involve organorhodium chemistry and a wealth of rhodium coordination compounds is known. For these and other areas, 103Rh NMR spectroscopy appears to be a very useful analytical tool. In this review, most of the literature concerning 103Rh NMR spectroscopy published from 1989 up to and including 2003 has been covered. After an introduction to several experimental methods for the detection of the insensitive 103Rh nucleus, a discussion of factors affecting the transition metal chemical shift is given. Computational aspects and calculations of chemical shifts are also briefly addressed. Next, the application of 103Rh NMR in coordination and organometallic chemistry is elaborated in more detail by highlighting recent developments in measurement and interpretation of 103Rh NMR data, in relation to rhodium-assisted reactions and homogeneous catalysis. The dependence of the 103Rh chemical shift on the ligands at rhodium in the first coordination sphere, on the complex geometry, oxidation state, temperature, solvent and concentration is treated. Several classes of compounds and special cases such as chiral rhodium compounds are reviewed. Finally, a section on scalar coupling to rhodium is provided. PMID:15307053

  2. Structural NMR of Protein Oligomers using Hybrid Methods

    PubMed Central

    Wang, Xu; Lee, Hsiau-Wei; Liu, Yizhou; Prestegard, James H.

    2010-01-01

    Solving structures of native oligomeric protein complexes using traditional high resolution NMR techniques remains challenging. However, increased utilization of computational platforms, and integration of information from less traditional NMR techniques with data from other complementary biophysical methods, promises to extend the boundary of NMR-applicable targets. This article reviews several of the techniques capable of providing less traditional and complementary structural information. In particular, the use of orientational constraints coming from residual dipolar couplings and residual chemical shift anisotropy offsets are shown to simplify the construction of models for oligomeric complexes, especially in cases of weak homo-dimers. Combining this orientational information with interaction site information supplied by computation, chemical shift perturbation, paramagnetic surface perturbation, cross-saturation and mass spectrometry allows high resolution models of the complexes to be constructed with relative ease. Non-NMR techniques, such as mass spectrometry, EPR and small angle X-ray scattering, are also expected to play increasingly important roles by offering alternative methods of probing the overall shape of the complex. Computational platforms capable of integrating information from multiple sources in the modeling process are also discussed in the article. And finally a new, detailed example on the determination of a chemokine tetramer structure will be used to illustrate how a non-traditional approach to oligomeric structure determination works in practice. PMID:21074622

  3. NMR studies of bond arrangements in alkali phosphate glasses

    SciTech Connect

    Alam, T.M.; Brow, R.K.

    1998-01-01

    Solid-state magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy has become a powerful tool for the investigation of local structure and medium range order in glasses. Previous {sup 31}P MAS NMR studies have detailed the local structure for a series of phosphate glasses. Phosphate tetrahedra within the glass network are commonly described using the Q{sup n} notation, where n = 0, 1, 2, 3 and represents the number of bridging oxygens attached to the phosphate. Using {sup 31}P MAS NMR different phosphate environments are readily identified and quantified. In this paper, the authors present a brief description of recent one dimensional (1D) {sup 6}Li, {sup 7}Li and {sup 31}P MAS experiments along with two-dimensional (2D) {sup 31}P exchange NMR experiments for a series of lithium ultraphosphate glasses. From the 2D exchange experiments the connectivities between different Q{sup n} phosphate tetrahedra were directly measured, while the 1D experiments provided a measure of the P-O-P bond angle distribution and lithium coordination number as a function of Li{sub 2}O concentration.

  4. Applications of 1H-NMR to Biodiesel Research

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Biodiesel is an alternative diesel fuel derived from vegetable oils, animal fats, or used cooking oils. It is produced by reacting these materials with an alcohol in the presence of a catalyst to give the corresponding mono-alkyl esters. 1H-NMR is a routine analytical method that has been used for...

  5. Time-resolved NMR studies of RNA folding.

    PubMed

    Fürtig, Boris; Buck, Janina; Manoharan, Vijayalaxmi; Bermel, Wolfgang; Jäschke, Andres; Wenter, Philipp; Pitsch, Stefan; Schwalbe, Harald

    The application of real-time NMR experiments to the study of RNA folding, as reviewed in this article, is relatively new. For many RNA folding events, current investigations suggest that the time scales are in the second to minute regime. In addition, the initial investigations suggest that different folding rates are observed for one structural transition may be due to the hierarchical folding units of RNA. Many of the experiments developed in the field of NMR of protein folding cannot directly be transferred to RNA: hydrogen exchange experiments outside the spectrometer cannot be applied since the intrinsic exchange rates are too fast in RNA, relaxation dispersion experiments on the other require faster structural transitions than those observed in RNA. On the other hand, information derived from time-resolved NMR experiments, namely the acquisition of native chemical shifts, can be readily interpreted in light of formation of a single long-range hydrogen bonding interaction. Together with mutational data that can readily be obtained for RNA and new ligation technologies that enhance site resolution even further, time-resolved NMR may become a powerful tool to decipher RNA folding. Such understanding will be of importance to understand the functions of coding and non-coding RNAs in cells. PMID:17595685

  6. Hydrogen Adsorption in Carbon-Based Materials Studied by NMR

    NASA Astrophysics Data System (ADS)

    Wu, Yue; Kleinhammes, Alfred; Anderson, Robert; Mao, Shenghua

    2007-03-01

    Hydrogen adsorption in carbon-based materials such as boron-doped graphite and boron-doped single-walled carbon nanotubes (SWNTs) were investigated by nuclear magnetic resonance (NMR). ^1H NMR is shown to be a sensitive and quantitative probe for detecting adsorbed gas molecules such as H2, methane, and ethane. NMR measurements were carried out in-situ under given H2 pressure up to a pressure of over 100 atm. From such ^1H NMR measurement, the amount of adsorbed H2 molecules was determined versus pressure. This gives an alternative method for measuring the adsorption isotherms where the H2 signature is identified based on spin properties rather than weight or volume as in gravimetric and volumetric measurements. The measurement shows that boron doping has a favorable effect on increasing the adsorption enthalpy of H2 in carbon-based systems. This work was done in collaboration with NREL and Department of Chemistry, University of Pennsylvania, within the DOE Center of Excellence on Carbon-based Hydrogen Storage Materials and is supported by DOE.

  7. Using NMR to Determine Protein Structure in Solution

    NASA Astrophysics Data System (ADS)

    Cavagnero, Silvia

    2003-02-01

    Nuclear magnetic resonance (NMR) is a marvelous spectroscopic technique that chemists, physicists, and biochemists routinely employ for their research around the world. This year half of the Nobel Prize for chemistry went to Kurt Wüthrich, who was recognized for the development of NMR-based techniques that lead to the structure determination of biomolecules in solution. In addition to implementing novel pulse sequences and software packages, Wüthrich also applied his methods to several biological systems of key importance to human health. These include the prion protein, which is heavily involved in the spongiform encephalopathy (best known as 'mad cow disease'), which recently caused numerous human deaths, particularly in the UK, due to ingestion of contaminated meat. Transverse relaxation optimized spectroscopy (TROSY) is the most intriguing new NMR method recently developed by Wüthrich and coworkers. This and other closely related pulse sequences promise to play a pivotal role in the extension of NMR to the conformational analysis of very large (up to the megadalton range) macromolecules and macromolecular complexes. More exciting new developments are expected in the near future.

  8. A Networked NMR Spectrometer: Configuring a Shared Instrument

    ERIC Educational Resources Information Center

    Alonso, David; Mutch, G. William; Wong, Peter; Warren, Steven; Barot, Bal; Kosinski, Jan; Sinton, Mark

    2005-01-01

    A model for a shared nuclear magnetic resonance spectroscopy (NMR) facility between a private university and two local community colleges is presented. The discussion of the components required for the shared facility, modes of data distribution, and overall effect on the curriculum is presented.

  9. NMR Shielding in Metals Using the Augmented Plane Wave Method

    PubMed Central

    2015-01-01

    We present calculations of solid state NMR magnetic shielding in metals, which includes both the orbital and the complete spin response of the system in a consistent way. The latter contains an induced spin-polarization of the core states and needs an all-electron self-consistent treatment. In particular, for transition metals, the spin hyperfine field originates not only from the polarization of the valence s-electrons, but the induced magnetic moment of the d-electrons polarizes the core s-states in opposite direction. The method is based on DFT and the augmented plane wave approach as implemented in the WIEN2k code. A comparison between calculated and measured NMR shifts indicates that first-principle calculations can obtain converged results and are more reliable than initially concluded based on previous publications. Nevertheless large k-meshes (up to 2 000 000 k-points in the full Brillouin-zone) and some Fermi-broadening are necessary. Our results show that, in general, both spin and orbital components of the NMR shielding must be evaluated in order to reproduce experimental shifts, because the orbital part cancels the shift of the usually highly ionic reference compound only for simple sp-elements but not for transition metals. This development paves the way for routine NMR calculations of metallic systems. PMID:26322148

  10. ECG gated NMR-CT for cardiovascular diseases

    SciTech Connect

    Nishikawa, J.; Ohtake, T.; Machida, K.; Iio, M.; Yoshimoto, N.; Sugimoto, T.

    1985-05-01

    The authors have been applying ECG gated NMR-CT to mainly patients with myocardial infarction (MI), and hypertrophic cardiomyopathy (HCM). Thirteen patients with MI, 8 with HCM and 5 without any heart diseases were studied by ECG gated NMR imaging (spin-echo technique, TR: depends on patient heart rate, TE: 35 and 70 msec.) with 0.35 T superconducting magnet. On NMR images (MRI), the authors examined the wall thickness, wall motion and T/sub 2/ relaxation time in the area of diseased myocardium. The lesions of old MI were depicted as the area of thin wall and T/sub 2/ relaxation time of those lesions were similar to the area of non-infarcted myocardium. The lesions of recent MI (up to 3.5 months from the recent attack) were shown as the same wall thickness as the non-infarcted myocardium and the area of prolonged T/sub 2/ relaxation time compared with that of non-infarcted myocardium. MRI demonstrated diffusely thick myocardium in all patients with HCM. T/sub 2/ relaxation time of the areas of HCM was almost the same as that of normal myocardium, and it's difference among each ventricular wall in patients with HCM was not statistically significant. The authors conclude that ECG gated NMR-CT offers 3-D morphological information of the heart without any contrast material nor radioisotopes. ECG gated MRI provides the useful informations to diagnose MI, especially in the differential diagnosis between old and recent MI.

  11. NMR of thin layers using a meanderline surface coil

    DOEpatents

    Cowgill, Donald F.

    2001-01-01

    A miniature meanderline sensor coil which extends the capabilities of nuclear magnetic resonance (NMR) to provide analysis of thin planar samples and surface layer geometries. The sensor coil allows standard NMR techniques to be used to examine thin planar (or curved) layers, extending NMRs utility to many problems of modern interest. This technique can be used to examine contact layers, non-destructively depth profile into films, or image multiple layers in a 3-dimensional sense. It lends itself to high resolution NMR techniques of magic angle spinning and thus can be used to examine the bonding and electronic structure in layered materials or to observe the chemistry associated with aging coatings. Coupling this sensor coil technology with an arrangement of small magnets will produce a penetrator probe for remote in-situ chemical analysis of groundwater or contaminant sediments. Alternatively, the sensor coil can be further miniaturized to provide sub-micron depth resolution within thin films or to orthoscopically examine living tissue. This thin-layer NMR technique using a stationary meanderline coil in a series-resonant circuit has been demonstrated and it has been determined that the flat meanderline geometry has about he same detection sensitivity as a solenoidal coil, but is specifically tailored to examine planar material layers, while avoiding signals from the bulk.

  12. NMR Studies of the Li-Mg-N-H Phases.

    NASA Astrophysics Data System (ADS)

    Bowman, Robert; Reiter, J. W.; Kulleck, J. G.; Hwang, S.-J.; Luo, Weifang

    2007-03-01

    Solid state NMR including magic-angle-spinning (MAS) and cross-polarization (CP) MAS experiments have been used to characterize various amide and imide phases containing Li and/or Mg. MAS-NMR spectra for the ^1H, ^6Li, ^7Li, and ^15N nuclei have been obtained to improve understanding on formation, processing, and degradation behavior. Only limited information could be obtained from the proton and ^7Li MAS-NMR spectra to due large dipolar interactions and small chemical shifts. However, more success was obtained from the ^6Li and ^15N nuclei although their very long spin-lattice relaxation times did impact signal acquisition times. For example, three distinct ^6Li peaks were resolved from LiNH2 phases that were clearly separated from the LiH secondary phase in these samples. While the ^15N spectra for LiNH2 phase in isotopically enriched samples exhibited only a single peak at least three distinct ^15N peaks were observed from the similarly enriched Mg amide samples. These differences will be related to crystal structures. The NMR spectra also revealed very little motion in these hydrides upon to nearly 500 K.

  13. Diffusional Properties of Methanogenic Granular Sludge: 1H NMR Characterization

    PubMed Central

    Lens, Piet N. L.; Gastesi, Rakel; Vergeldt, Frank; van Aelst, Adriaan C.; Pisabarro, Antonio G.; Van As, Henk

    2003-01-01

    The diffusive properties of anaerobic methanogenic and sulfidogenic aggregates present in wastewater treatment bioreactors were studied using diffusion analysis by relaxation time-separated pulsed-field gradient nuclear magnetic resonance (NMR) spectroscopy and NMR imaging. NMR spectroscopy measurements were performed at 22°C with 10 ml of granular sludge at a magnetic field strength of 0.5 T (20 MHz resonance frequency for protons). Self-diffusion coefficients of H2O in the investigated series of mesophilic aggregates were found to be 51 to 78% lower than the self-diffusion coefficient of free water. Interestingly, self-diffusion coefficients of H2O were independent of the aggregate size for the size fractions investigated. Diffusional transport occurred faster in aggregates growing under nutrient-rich conditions (e.g., the bottom of a reactor) or at high (55°C) temperatures than in aggregates cultivated in nutrient-poor conditions or at low (10°C) temperatures. Exposure of aggregates to 2.5% glutaraldehyde or heat (70 or 90°C for 30 min) modified the diffusional transport up to 20%. In contrast, deactivation of aggregates by HgCl2 did not affect the H2O self-diffusion coefficient in aggregates. Analysis of NMR images of a single aggregate shows that methanogenic aggregates possess a spin-spin relaxation time and self-diffusion coefficient distribution, which are due to both physical (porosity) and chemical (metal sulfide precipitates) factors. PMID:14602624

  14. NMR Studies of Biomass and its Reaction Products

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Biomass refers to biological material derived from living or recently living organisms, such as wood, agricultural products and wastes, and alcohol fuels. An increasingly popular R&D approach is to convert biomass into industrial polymers or chemicals. NMR is an excellent technique for the character...

  15. Single bead detection with an NMR microcapillary probe

    NASA Astrophysics Data System (ADS)

    Nakashima, Yoshihiro; Boss, Michael; Russek, Stephen E.; Moreland, John

    2012-11-01

    We have developed a nuclear magnetic resonance (NMR) microcapillary probe for the detection of single magnetic microbeads. The geometry of the probe has been optimized so that the signal from the background water has a similar magnitude compared to the signal from the dephased water nearby a single magnetic bead within the probe detector coil. In addition, the RF field of the coil must be uniform within the effective range of the magnetic bead. Three different RF probes were tested in a 7 T (300 MHz) pulsed NMR spectrometer with sample volumes ranging from 5 nL down to 1 nL. The 1 nL probe had a single-shot signal-to-noise ratio (SNR) for pure water of 27 and a volume resolution that exhibits a 600-fold improvement over a conventional (5 mm tube) NMR probe with a sample volume of 18 μL. This allowed for the detection of a 1 μm magnetite/polystyrene bead (m = 2 × 10-14 A m2) with an estimated experimental SNR of 30. Simulations of the NMR spectra for the different coil geometries and positions of the bead within the coil were developed that include the B0 shift near a single bead, the inhomogeneity of the coils, the local coil sensitivity, the skin effect of the coil conductor, and quantitated estimates of the proximity effect between coil windings.

  16. NMR studies of structure and dynamics in fruit cuticle polyesters.

    PubMed

    Stark, R E; Yan, B; Ray, A K; Chen, Z; Fang, X; Garbow, J R

    2000-05-01

    Cutin and suberin are support polymers involved in waterproofing the leaves and fruits of higher plants, regulating the flow of nutrients among various plant organs, and minimizing the deleterious impact of microbial pathogens. Despite the complexity and intractable nature of these plant biopolyesters, their molecular structure and development are amenable to study by suitable solid-state and solution-state NMR techniques. Interactions of tomato cutin with water were examined by solid-state 2H and 13C NMR, showing that water films enhance rapid segmental motions of the acyl chains and are associated with a fivefold increase in surface elasticity upon cutin hydration. The suberization of wounded potato tissues was studied by solid-state 13C NMR, revealing the likely phenylpropanoid structures that permit dense cross-linking of the suberin structure and their proximity to the cell-wall polysaccharides. Finally, two new approaches were developed to elucidate the molecular structures of these biopolymers: partial depolymerization followed by spectroscopic analysis of the soluble oligomers; and swelling of the intact materials followed by magic-angle spinning (MAS) NMR analysis. PMID:10811427

  17. Detecting and Quantifying Organic Contaminants in Sediments with NMR

    NASA Astrophysics Data System (ADS)

    Fay, E. L.; Knight, R. J.

    2015-12-01

    Nuclear magnetic resonance (NMR) methods have the potential to detect and monitor free-phase organic contaminants in sediments, both in the laboratory and in the field. NMR directly detects signal from hydrogen-bearing fluids; the signal amplitude is proportional to the total amount of hydrogen present, while the signal decay rate provides information about fluid properties and interactions with the surrounding sediments. Contrasting relaxation times (T2) or diffusion coefficients (D) allow the separation of water signal from contaminant signal. In this work, we conduct a laboratory study to assess the use of NMR measurements to detect and quantify diesel, gasoline, crude oil, and tri-chloroethylene in sediments. We compare the T2 distributions for sediments containing only water, only contaminant, and both water and contaminant, confirming that the identification and quantification of contaminants using T2 data alone is limited by overlapping water and contaminant T2 distributions in some sediments. We leverage the contrast between the diffusion coefficient of water and that of diesel and crude oil to separate contaminant signal from water signal in D-T2 maps. D-T2 distributions are measured both using a pulsed gradient method and a static gradient method similar to methods used with logging tools, allowing us to compare the ability of each method to quantify diesel and crude oil when water is also present. There is the potential to apply these methods to characterize and monitor contaminated sites using commercially available NMR logging tools.

  18. Investigations of silicone breast implants with the NMR-MOUSE.

    PubMed

    Krüger, Mirko; Schwarz, Annett; Blümich, Bernhard

    2007-02-01

    Silicone breast implants are used for breast augmentation and breast reconstruction. The issues of concern associated with such implants are: (a) the quality control of each implant before implantation, and (b) the detection of implant bleeding after implantation. We have studied the use of the Nuclear Magnetic Resonance-MObile Universal Surface Explorer (NMR-MOUSE) for the nondestructive testing of (a) the quality of implant shells, and (b) changes in implant gel due to leakage of body fluid into the implant. Depth profiles measured nondestructively through implant shells at different positions of each implant by the Profile NMR-MOUSE assured good reproducibility of the quality and thickness of different shell layers. The leakage of implants upon rupture was mimicked by observing changes in the transverse NMR relaxation time of the implant gel upon ingress of physiological saline solution and safflower oil through the rupture. Results demonstrate that nondestructive testing with unilateral NMR is a potential method for use in the quality control of implants and for the screening of implants for rupture after implantation. PMID:17275616

  19. Exploiting Image Registration for Automated Resonance Assignment in NMR

    PubMed Central

    Strickland, Madeleine; Stephens, Thomas; Liu, Jian; Tjandra, Nico

    2015-01-01

    Summary Analysis of protein NMR data involves the assignment of resonance peaks in a number of multidimensional data sets. To establish resonance assignment a three-dimensional search is used to match a pair of common variables, such as chemical shifts of the same spin system, in different NMR spectra. We show that by displaying the variables to be compared in two-dimensional plots the process can be simplified. Moreover, by utilizing a fast Fourier transform (FFT) cross-correlation algorithm, more common to the field of image registration or pattern matching, we can automate this process. Here, we use sequential NMR backbone assignment as an example to show that the combination of correlation plots and segmented pattern matching establishes fast backbone assignment in fifteen proteins of varying sizes. For example, the 265-residue RalBP1 protein was 95.4% correctly assigned in 10 seconds. The same concept can be applied to any multidimensional NMR data set where analysis comprises the comparison of two variables. This modular and robust approach offers high efficiency with excellent computational scalability and could be easily incorporated into existing assignment software. PMID:25828257

  20. Cation Hydration Constants by Proton NMR: A Physical Chemistry Experiment.

    ERIC Educational Resources Information Center

    Smith, Robert L.; And Others

    1988-01-01

    Studies the polarization effect on water by cations and anions. Describes an experiment to illustrate the polarization effect of sodium, lithium, calcium, and strontium ions on the water molecule in the hydration spheres of the ions. Analysis is performed by proton NMR. (MVL)

  1. Nondestructive NMR technique for moisture determination in radioactive materials.

    SciTech Connect

    Aumeier, S.; Gerald, R.E. II; Growney, E.; Nunez, L.; Kaminski, M.

    1998-12-04

    This progress report focuses on experimental and computational studies used to evaluate nuclear magnetic resonance (NMR) spectroscopy and magnetic resonance imaging (MRI) for detecting, quantifying, and monitoring hydrogen and other magnetically active nuclei ({sup 3}H, {sup 3}He, {sup 239}Pu, {sup 241}Pu) in Spent nuclear fuels and packaging materials. The detection of moisture by using a toroid cavity NMR imager has been demonstrated in SiO{sub 2} and UO{sub 2} systems. The total moisture was quantified by means of {sup 1}H NMR detection of H{sub 2}O with a sensitivity of 100 ppm. In addition, an MRI technique that was used to determine the moisture distribution also enabled investigators to discriminate between bulk and stationary water sorbed on the particles. This imaging feature is unavailable in any other nondestructive assay (NDA) technique. Following the initial success of this program, the NMR detector volume was scaled up from the original design by a factor of 2000. The capacity of this detector exceeds the size specified by DOE-STD-3013-96.

  2. Development and Use of a Virtual NMR Facility

    NASA Astrophysics Data System (ADS)

    Keating, Kelly A.; Myers, James D.; Pelton, Jeffrey G.; Bair, Raymond A.; Wemmer, David E.; Ellis, Paul D.

    2000-03-01

    We have developed a "virtual NMR facility" (VNMRF) to enhance access to the NMR spectrometers in Pacific Northwest National Laboratory's Environmental Molecular Sciences Laboratory (EMSL). We use the term virtual facility to describe a real NMR facility made accessible via the Internet. The VNMRF combines secure remote operation of the EMSL's NMR spectrometers over the Internet with real-time videoconferencing, remotely controlled laboratory cameras, real-time computer display sharing, a Web-based electronic laboratory notebook, and other capabilities. Remote VNMRF users can see and converse with EMSL researchers, directly and securely control the EMSL spectrometers, and collaboratively analyze results. A customized Electronic Laboratory Notebook allows interactive Web-based access to group notes, experimental parameters, proposed molecular structures, and other aspects of a research project. This paper describes our experience developing a VNMRF and details the specific capabilities available through the EMSL VNMRF. We show how the VNMRF has evolved during a test project and present an evaluation of its impact in the EMSL and its potential as a model for other scientific facilities. All Collaboratory software used in the VNMRF is freely available from http://www.emsl.pnl.gov:2080/docs/collab.

  3. NMR in rotating magnetic fields: Magic angle field spinning

    SciTech Connect

    Sakellariou, D.; Meriles, C.; Martin, R.; Pines, A.

    2004-09-10

    Magic angle sample spinning has been one of the cornerstones in high-resolution solid state NMR. Spinning frequencies nowadays have increased by at least one order of magnitude over the ones used in the first experiments and the technique has gained tremendous popularity. It is currently a routine procedure in solid-state NMR, high-resolution liquid-state NMR and solid-state MRI. The technique enhances the spectral resolution by averaging away rank 2 anisotropic spin interactions thereby producing isotropic-like spectra with resolved chemical shifts and scalar couplings. Andrew proposed that it should be possible to induce similar effects in a static sample if the direction of the magnetic field is varied, e.g., magic-angle rotation of the B0 field (B0-MAS) and this has been recently demonstrated using electromagnetic field rotation. Here we discuss on the possibilities to perform field rotation using alternative hardware, together with spectroscopic methods to recover isotropic resolution even in cases where the field is not rotating at the magic angle. Extension to higher magnetic fields would be beneficial in situations where the physical manipulation of the sample is inconvenient or impossible. Such situations occur often in materials or biomedical samples where ''ex-situ'' NMR spectroscopy and imaging analysis is needed.

  4. MULTIVARIATE CURVE RESOLUTION OF NMR SPECTROSCOPY METABONOMIC DATA

    EPA Science Inventory

    Sandia National Laboratories is working with the EPA to evaluate and develop mathematical tools for analysis of the collected NMR spectroscopy data. Initially, we have focused on the use of Multivariate Curve Resolution (MCR) also known as molecular factor analysis (MFA), a tech...

  5. NMR and NQR study of the thermodynamically stable quasicrystals

    SciTech Connect

    Shastri, A.

    1995-02-10

    {sup 27}Al and {sup 61,65}Cu NMR measurements are reported for powder samples of stable AlCuFe and AlCuRu icosahedral quasicrystals and their crystalline approximants, and for a AlPdMn single grain quasicrystal. Furthermore, {sup 27}Al NQR spectra at 4.2 K have been observed in the AlCuFe and AlCuRu samples. From the quadrupole perturbed NMR spectra at different magnetic fields, and from the zero field NQR spectra, a wide distribution of local electric field gradient (EFG) tensor components and principal axis system orientations was found at the Al site. A model EFG calculation based on a 1/1 AlCuFe approximant was successful in explaining the observed NQR spectra. It is concluded that the average local gradient is largely determined by the p-electron wave function at the Al site, while the width of the distribution is due to the lattice contribution to the EFG. Comparison of {sup 63}Cu NMR with {sup 27}Al NMR shows that the EFG distribution at the two sites is similar, but that the electronic contribution to the EFG is considerably smaller at the Cu site, in agreement with a more s-type wave function of the conduction electrons.

  6. NMR spin relaxation rates in the Heisenberg bilayer

    NASA Astrophysics Data System (ADS)

    Mendes, Tiago; Curro, Nicholas; Scalettar, Richard; Paiva, Thereza; Dos Santos, Raimundo R.

    One of the striking features of heavy fermions is the fact that in the vicinity of a quantum phase transition these systems exhibit the breakdown of Fermi-liquid behavior and superconductivity. Nuclear magnetic resonance (NMR) expirements play an important role in the study of these phenomena. Measurements of NMR spin relaxation rates and Knight shift, for instance, can be used to probe the electronic spin susceptibility of these systems. Here we studied the NMR response of the Heisenberg bilayer model. In this model, it is well known that the increase of the interplane coupling between the planes, Jperp, supresses the antiferromagnetic order at a quantum critical point (QCP). We use stochastic series expansion (SSE) and the maximum-entropy analytic continuation method to calculate the NMR spin lattice relaxation rate 1 /T1 and the spin echo decay 1 /T2 G as function of Jperp. The spin echo decay, T2 G increases for small Jperp, due to the increase of the order parameter, and then vanishes abruptly in the QCP. The effects of Jperp dilution disorder in the QCP and the relaxation rates are also discussed. This research was supported by the NNSA Grant Number DE-NA 0002908, and Ciência sem fronteiras program/CNPQ.

  7. X-ray CT and NMR imaging of rocks

    SciTech Connect

    Vinegar, H.J.

    1986-03-01

    In little more than a decade, X-ray computerized tomography (CT) and nuclear magnetic resonance (NMR) imaging have become the premier modalities of medical radiology. Both of these imaging techniques also promise to be useful tools in petrophysics and reservoir engineering, because CT and NMR can nondestructively image a host of physical and chemical properties of porous rocks and multiple fluid phases contained within their pores. The images are taken within seconds to minutes, at reservoir temperatures and pressures, with spatial resolution on the millimeter and submillimeter level. The physical properties imaged by the two techniques are complementary. CT images bulk density and effective atomic number. NMR images the nuclide concentration, M/sub 0/, of a variety of nuclei (/sup 1/H, /sup 19/F, /sup 23/Na, /sup 31/P, etc.), their longitudinal and transverse relaxation-time curves (t/sub 1/ and t/sub 2/), and their chemical shift spectra. In rocks, CT images both rock matrix and pore fluids, while NMR images only mobile fluids and the interactions of these mobile fluids with the confining surfaces of the pores.

  8. NMR spectroscopy and perfusion of mammalian cells using surface microprobes.

    PubMed

    Ehrmann, Klaus; Pataky, Kristopher; Stettler, Matthieu; Wurm, Florian Maria; Brugger, Jürgen; Besse, Pierre-André; Popovic, Radivoje

    2007-03-01

    NMR spectra of mammalian cells are taken using surface microprobes that are based on microfabricated planar coils. The surface microprobe resembles a miniaturized Petri dish commonly used in biological research. The diameter of the planar coils is 1 mm. Chinese Hamster Ovaries are immobilized in a uniform layer on the microprobe surface or patterned by an ink-jet printer in the centre of the microcoil, where the rf-field of the planar microcoil is most uniform. The acquired NMR spectra show the prevalent metabolites found in mammalian cells. The volumes of the detected samples range from 25 nL to 1 nL (or 50,000 to 1800 cells). With an extended set-up that provides fluid inlets and outlets to the microprobe, the cells can be perfused within the NMR-magnet while constantly taking NMR spectra. Perfusion of the cells opens the way to increased cell viability for long acquisitions or to analysis of the cells' response to environmental change. PMID:17330170

  9. Calculation of NMR lineshapes for Ba-Al-Ge clathrates

    NASA Astrophysics Data System (ADS)

    Rodriguez, Sergio; Gou, Weiping; Ross, Joseph

    2008-10-01

    Clathrates consist of Si, Ge, or Sn cages in a crystalline framework, with guest atoms inside the cages. They have gained interest due to thermoelectric properties suitable for potential device application. To understand Al substitutional configurations, we calculated Al NMR line shapes for several structures with compositions Ba8Ge46-x-yAlxy for x=3,8,11,12,16,24; y=2,3; where represents a vacancy. The results were obtained by calculating Electric Field Gradients (EFG) for Al sites of type-I clathrates assuming an ordered superstructure of vacancies and framework occupation. We used ab initio methods in the Generalized Gradient Approximation as implemented by the WIEN2k program, and used the results to simulate NMR lineshapes numerically. These were compared to our previously reported NMR lineshapes. In the case of Ba8Ge31Al123 four Al sites in the superstructure include two sites with small EFG where the vacancy is far away and two sites with large EFG with a vacancy adjacent to Al. Assuming a larger Knight shift for sites next to vacancies, we obtain good agreement with NMR experimental results for reduced-Al Ba8Ge34Al12, while for the Zintl phase Ba8Ge30Al16 we obtain good agreement with no spontaneous vacancies. We infer that Al prefers locations close to vacancies rather than random occupation. This work was supported by Robert A. Welch Foundation (Grant A-1526).

  10. Adiabatic single scan two-dimensional NMR spectrocopy.

    PubMed

    Pelupessy, Philippe

    2003-10-01

    New excitation schemes, based on the use adiabatic pulses, for single scan two-dimensional NMR experiments (Frydman et al., Proc. Nat. Acad. Sci. 2002, 99, 15 858-15 862) are introduced. The advantages are discussed. Applications in homo- and heteronuclear experiments are presented. PMID:14519020

  11. Novel Dodecaarylporphyrins: Synthesis and Variable Temperature NMR Studies

    SciTech Connect

    Cancilla, Mark; Lebrilla, Carlito; Ma, Jian-Guo; Medforth, Craig J.; Muzzi, Cinzia M.; Shelnutt, John A.; Smith, Kevin M.; Voss, Lisa

    1999-05-05

    An investigation of the synthesis of novel dodecaarylporphyrins using the Suzuki coupling reaction of arylboronic acids with octabromotetraarylporphyrins is reported. Studies of the dynamic properties of these new porphyrins using variable temperature (VT) 1H NMR spectroscopy and molecular mechanics provide interesting insights into their dynamic properties, including the first determination of {beta} aryl rotation in a porphyrin system.

  12. Extended hopane derivatives in sediments - Identification by H-1 NMR

    NASA Technical Reports Server (NTRS)

    Taylor, J.; Wardroper, A. M. K.; Maxwell, J. R.

    1980-01-01

    Sedimentary C32 hopanoic acid, one of the most abundant in nature and of probable bacterial origin, has been isolated for the first time as a single component and characterized by H-1 NMR. The 17 alpha H, 21 beta H configuration of the C31 alkane has been similarly confirmed.

  13. Solid-State NMR Spectroscopy for the Physical Chemistry Laboratory

    ERIC Educational Resources Information Center

    Kinnun, Jacob J.; Leftin, Avigdor; Brown, Michael F.

    2013-01-01

    Solid-state nuclear magnetic resonance (NMR) spectroscopy finds growing application to inorganic and organic materials, biological samples, polymers, proteins, and cellular membranes. However, this technique is often neither included in laboratory curricula nor typically covered in undergraduate courses. On the other hand, spectroscopy and…

  14. Hepatic cancer: Correlative imaging with radioimmunodetection, NMR, and TCT

    SciTech Connect

    De Lund, F.H.; Lieber, A.; Ram, M.D.; Goldenberg, D.M.

    1984-01-01

    The purpose of this study was to compare the sensitivity of radioimmunodetection (RAID) imaging and nuclear magnetic resonance imaging in the detection of hepatic tumors. Twelve consecutive patients with metastatic (11) or primary (1) carcinoma of the liver were imaged concurrently with labeled antibodies-to-tumor antigens and by nuclear magnetic resonance. Evidence of hepatic tumors was corrected with other diagnostic procedures including TCT. Eleven patients were imaged with I-131 labeled antibodies to CEA, CSAP and one with I-131 labeled antibodies to AFP. Polyclonal, monoclonal, and Fab'/sub 2/ antibodies were used. The preparation and labeling of the antibodies have been described previously. Each patient received 2-3 mCi of labeled antibodies and was imaged at 24 to 48 hrs. Nontarget radioactivity was diminished by other radionuclides simulating nontumor distribution using a computer subtraction technique. NMR images were obtained with a 0.15T resistive instrument. In all twelve patients hepatic tumor was diagnosed by RAID. Nine of the hepatic tumors were confirmed by other methods. NMR demonstrated four positive findings in these nine. Computerized tomography detected tumors in three of the nine patients at the time of the first RAID examination, and subsequently in one more patient when RAID and NMR examinations were performed concurrently. In this series of patients the detection of hepatic cancer by RAID showed twice the sensitivity of NMR or TCT.

  15. NMR at the Picomole Level of a DNA Adduct

    PubMed Central

    Kautz, Roger; Wang, Poguang; Giese, Roger W.

    2014-01-01

    We investigate the limit of detection for obtaining NMR data of a DNA adduct using modern microscale NMR instrumentation, once the adduct has been isolated at the pmol level. Eighty nanograms (130 pmol) of a DNA adduct standard, N-(2′-deoxyguanosin-8-yl)-2-acetylaminofluorene 5′-monophosphate (AAF-dGMP), in 1.5 μL of D2O with 10% methanol-d4, in a vial, was completely picked up as a droplet suspended in a fluorocarbon liquid, and loaded efficiently into a microcoil probe. This work demonstrates a practical manual method of droplet microfluidic sample loading, previously demonstrated using automated equipment, which provides a several-fold advantage over conventional flow injection. Eliminating dilution during injection and confining the sample into the observed volume realizes the full theoretical mass sensitivity of a microcoil, comparable to a micro-cryo probe. With 80 ng, an NMR spectrum acquired over 40 hr showed all of the resonances seen in a standard spectrum of AAF-dGMP, with a S/N of at least 10, despite broadening due to previously-noted effects of conformational exchange. Also a 2D TOCSY spectrum (total correlation spectroscopy) was acquired on 1.6 μg in 18 hr. This work helps to define the utility of NMR in combination with other analytical methods for the structural characterization of a small amount of a DNA adduct. PMID:24028148

  16. Noise figure characterization of preamplifiers at NMR frequencies

    NASA Astrophysics Data System (ADS)

    Nordmeyer-Massner, J. A.; De Zanche, N.; Pruessmann, K. P.

    2011-05-01

    A method for characterizing the noise figure of preamplifiers at NMR frequencies is presented. The noise figure of preamplifiers as used for NMR and MRI detection varies with source impedance and with the operating frequency. Therefore, to characterize a preamplifier's noise behavior, it is necessary to perform noise measurements at the targeted frequency while varying the source impedance with high accuracy. At high radiofrequencies, such impedance variation is typically achieved with transmission-line tuners, which however are not available for the relatively low range of typical NMR frequencies. To solve this issue, this work describes an alternative approach that relies on lumped-element circuits for impedance manipulation. It is shown that, using a fixed-impedance noise source and suitable ENR correction, this approach permits noise figure characterization for NMR and MRI purposes. The method is demonstrated for two preamplifiers, a generic BF998 MOSFET module and an MRI-dedicated, integrated preamplifier, which were both studied at 128 MHz, i.e., at the Larmor frequency of protons at 3 Tesla. Variations in noise figure of 0.01 dB or less over repeated measurements reflect high precision even for small noise figures in the order of 0.4 dB. For validation, large sets of measured noise figure values are shown to be consistent with the general noise-parameter model of linear two-ports. Finally, the measured noise characteristics of the superior preamplifier are illustrated by SNR measurements in MRI data.

  17. Advancements in waste water characterization through NMR spectroscopy: review.

    PubMed

    Alves Filho, Elenilson G; Alexandre e Silva, Lorena M; Ferreira, Antonio G

    2015-09-01

    There are numerous organic pollutants that lead to several types of ecosystem damage and threaten human health. Wastewater treatment plants are responsible for the removal of natural and anthropogenic pollutants from the sewage, and because of this function, they play an important role in the protection of human health and the environment. Nuclear magnetic resonance (NMR) has proven to be a valuable analytical tool as a result of its versatility in characterizing both overall chemical composition as well as individual species in a wide range of mixtures. In addition, NMR can provide physical information (rigidity, dynamics, etc.) as well as permit in depth quantification. Hyphenation with other techniques such as liquid chromatography, solid phase extraction and mass spectrometry creates unprecedented capabilities for the identification of novel and unknown chemical species. Thus, NMR is widely used in the study of different components of wastewater, such as complex organic matter (fulvic and humic acids), sludge and wastewater. This review article summarizes the NMR spectroscopy methods applied in studies of organic pollutants from wastewater to provide an exhaustive review of the literature as well as a guide for readers interested in this topic. PMID:25280056

  18. Maximum entropy signal processing in practical NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Sibisi, Sibusiso; Skilling, John; Brereton, Richard G.; Laue, Ernest D.; Staunton, James

    1984-10-01

    NMR spectroscopy is intrinsically insensitive, a frequently serious limitation especially in biochemical applications where sample size is limited and compounds may be too insoluble or unstable for data to be accumulated over long periods. Fourier transform (FT) NMR was developed by Ernst1 to speed up the accumulation of useful data, dramatically improving the quality of spectra obtained in a given observing time by recording the free induction decay (FID) data directly in time, at the cost of requiring numerical processing. Ernst also proposed that more information could be obtained from the spectrum if the FID was multiplied by a suitable apodizing function before being Fourier transformed. For example (see ref. 2), an increase in sensitivity can result from the use of a matched filter1, whereas an increase in resolution can be achieved by the use of gaussian multiplication1,3, application of sine bells4-8 or convolution difference9. These methods are now used routinely in NMR data processing. The maximum entropy method (MEM)10 is theoretically capable of achieving simultaneous enhancement in both respects11, and this has been borne out in practice in other fields where it has been applied. However, this technique requires relatively heavy computation. We describe here the first practical application of MEM to NMR, and we analyse 13C and 1H NMR spectra of 2-vinyl pyridine. Compared with conventional spectra, MEM gives considerable suppression of noise, accompanied by significant resolution enhancement. Multiplets in the 1H spectra are resolved better leading to improved visual clarity.

  19. Study of correlations in molecular motion by multiple quantum NMR

    SciTech Connect

    Tang, J.H.

    1981-11-01

    Nuclear magnetic resonance is a very useful tool for characterizing molecular configurations through the measurement of transition frequencies and dipolar couplings. The measurement of spectral lineshapes, spin-lattice relaxation times, and transverse relaxation times also provide us with valuable information about correlations in molecular motion. The new technique of multiple quantum nuclear magnetic resonance has numerous advantages over the conventional single quantum NMR techniques in obtaining information about static and dynamic interactions of coupled spin systems. In the first two chapters, the theoretical background of spin Hamiltonians and the density matrix formalism of multiple quantum NMR is discussed. The creation and detection of multiple quantum coherence by multiple pulse sequence are discussed. Prototype multiple quantum spectra of oriented benzene are presented. Redfield relaxation theory and the application of multiple quantum NMR to the study of correlations in fluctuations are presented. A specific example of an oriented methyl group relaxed by paramagnetic impurities is studied in detail. The study of possible correlated motion between two coupled methyl groups by multiple quantum NMR is presented. For a six spin system it is shown that the four-quantum spectrum is sensitive to two-body correlations, and serves a ready test of correlated motion. The study of the spin-lattice dynamics of orienting or tunneling methyl groups (CH/sub 3/ and CD/sub 3/) at low temperatures is presented. The anisotropic spin-lattice relaxation of deuterated hexamethylbenzene, caused by the sixfold reorientation of the molecules, is investigated, and the NMR spectrometers and other experimental details are discussed.

  20. Solid state NMR strategy for characterizing native membrane protein structures.

    PubMed

    Murray, Dylan T; Das, Nabanita; Cross, Timothy A

    2013-09-17

    Unlike water soluble proteins, the structures of helical transmembrane proteins depend on a very complex environment. These proteins sit in the midst of dramatic electrical and chemical gradients and are often subject to variations in the lateral pressure profile, order parameters, dielectric constant, and other properties. Solid state NMR is a collection of tools that can characterize high resolution membrane protein structure in this environment. Indeed, prior work has shown that this complex environment significantly influences transmembrane protein structure. Therefore, it is important to characterize such structures under conditions that closely resemble its native environment. Researchers have used two approaches to gain protein structural restraints via solid state NMR spectroscopy. The more traditional approach uses magic angle sample spinning to generate isotropic chemical shifts, much like solution NMR. As with solution NMR, researchers can analyze the backbone chemical shifts to obtain torsional restraints. They can also examine nuclear spin interactions between nearby atoms to obtain distances between atomic sites. Unfortunately, for membrane proteins in lipid preparations, the spectral resolution is not adequate to obtain complete resonance assignments. Researchers have developed another approach for gaining structural restraints from membrane proteins: the use of uniformly oriented lipid bilayers, which provides a method for obtaining high resolution orientational restraints. When the bilayers are aligned with respect to the magnetic field of the NMR spectrometer, researchers can obtain orientational restraints in which atomic sites in the protein are restrained relative to the alignment axis. However, this approach does not allow researchers to determine the relative packing between helices. By combining the two approaches, we can take advantage of the information acquired from each technique to minimize the challenges and maximize the quality of the